OK, I found a dvr-ms instruction so I added
			<!-- For dvr-ms files force mpeg2video transcoding to fix monotone timestamps problems-->
			<Video targetContainer="mpegts" targetACodec="ac3" forceVTranscoding="true">
				<Matches container="asf" vCodec="mpeg2video" />
			</Video>
Now that triggers the transcode but then it gives an error. I ran the ffmpeg instruction found in the log file manually and here is what it does:
ffmpeg.exe -threads 2 -i "E:\Recorded TV\One Life to Live_KGODT-DT_24_01_2011_13_58_33.dvr-ms" -y -vcodec copy -copyts -acodec copy -map 0:2 -map 0:1 -sn -f mpegts "E:\Serviio\transcoding-temp-17901-MPEG2TS.stf"
C:\Program Files\Serviio>cd lib
C:\Program Files\Serviio\lib>ffmpeg.exe -threads 2 -i "E:\Recorded TV\One Life t
o Live_KGODT-DT_24_01_2011_13_58_33.dvr-ms" -y -vcodec copy -copyts -acodec copy
 -map 0:2 -map 0:1 -sn -f mpegts "E:\Serviio\transcoding-temp-17901-MPEG2TS.stf"
FFmpeg version UNKNOWN, Copyright (c) 2000-2011 the FFmpeg developers
  built on Jan 10 2011 21:46:22 with gcc 4.4.2
  configuration: --enable-static --disable-shared --disable-shared --disable-ffp
lay --disable-ffserver --enable-memalign-hack --enable-libmp3lame --arch=x86 --e
nable-runtime-cpudetect --enable-w32threads --target-os=mingw32 --cross-prefix=i
686-mingw32-
  libavutil     50.36. 0 / 50.36. 0
  libavcore      0.16. 0 /  0.16. 0
  libavcodec    52.108. 0 / 52.108. 0
  libavformat   52.92. 0 / 52.92. 0
  libavdevice   52. 2. 3 / 52. 2. 3
  libavfilter    1.72. 0 /  1.72. 0
  libswscale     0.12. 0 /  0.12. 0
[mpeg2video @ 016e5a40] mpeg_decode_postinit() failure
    Last message repeated 34 times
Input #0, asf, from 'E:\Recorded TV\One Life to Live_KGODT-DT_24_01_2011_13_58_3
3.dvr-ms':
  Metadata:
    DVR Index Granularity: 500
    WM/SubTitle     :
    WM/SubTitleDescription: Starr is surprised at her father's support for James
; Cristian learns Layla and Steffen slept together; Shaun agrees to help Darren
win Destiny back.
    genre           : Soap Opera,Series
    WM/MediaCredits : Erika Slezak/Robin Strasser/Trevor St. John/Michael Easton
/Robert S. Woods/Kassie DePaiva/Kristen Alderson/Melissa Archer/John-Paul Lavois
ier/Brandon Buddy/Bree Williamson/David Fumero/Kamar de los Reyes/John Brotherto
n/Farah Fath/BethAnn Bonner/Kathy Brier/Jerry ver Dorn/David Chisum/Catherine Hi
ckland;;;
    WM/ParentalRating: TV-PG
    WM/ParentalRatingReason:
    WM/ProviderRating:
    WM/OriginalReleaseTime: 0001-01-01T00:00:00.0000000-08:00
    WM/MediaStationCallSign: KGODT-DT
    WM/MediaStationName: KGODT (KGO-DT)
    WM/MediaNetworkAffiliation: ABC Affiliate
    WM/MediaOriginalChannel: 2807
    WM/MediaOriginalBroadcastDateTime: 2011-01-24T00:00:00.0000000-08:00
    WM/WMRVServiceID: ATSC-KGODT-80-7
    WM/WMRVProgramID: OFlpbHv+0T2uMT0iw7jF5g==
    WM/MediaOriginalRunTime: 1640261
    WM/WMRVEncodeTime: 1844674
    WM/MediaIsStereo: 1
    WM/VideoClosedCaptioning: 1
    WM/MediaIsRepeat: 0
    WM/MediaIsLive  : 0
    WM/MediaIsTape  : 0
    WM/MediaIsDelay : 0
    WM/MediaIsSubtitled: 0
    WM/MediaIsPremiere: 0
    WM/MediaIsFinale: 0
    WM/MediaIsSAP   : 0
    WM/WMRVRequestID: 98
    WM/WMRVScheduleItemID: 186
    WM/WMRVQuality  : 3
    WM/WMRVOriginalSoftPrePadding: 0
    WM/WMRVOriginalSoftPostPadding: 180
    WM/WMRVActualSoftPrePadding: 0
    WM/WMRVHardPrePadding: 0
    WM/Provider     : Zap2it
    WM/ProviderCopyright: © 2011 Microsoft Corporation. All Rights Reserved. Te
rms of Service: 
http://go.microsoft.com/fwlink/?LinkId=8430    WM/WMRVEndTime  : 1844674
    WM/WMRVExpirationDate: 1844674
    WM/WMRVBitrate  : 0
    WM/WMRVKeepUntil: 184
    WM/WMRVHardPostPadding: 0
    WM/WMRVActualSoftPostPadding: 180
    WM/WMRVContentProtectedPercent: 0
    WM/WMRVInBandRatingSystem: 255
    WM/WMRVInBandRatingLevel: 255
    WM/WMRVInBandRatingAttributes: 0
    WM/WMRVWatched  : 0
    WM/WMRVATSCContent: 1
    WM/WMRVDTVContent: 1
    WM/WMRVHDContent: 0
    WM/WMRVContentProtected: 0
    WMFSDKVersion   : 11.0.5721.5275
    WMFSDKNeeded    : 0.0.0.0000
    VBR Peak        : 159
    IsVBR           : 1
    title           : One Life to Live
    artist          :
    copyright       :
    comment         :
  Duration: 00:04:26.75, start: 6.311000, bitrate: 10924 kb/s
    Stream #0.0: Invalid Codec type -1
    Stream #0.1: Audio: ac3, 48000 Hz, 5.1, s16, 384 kb/s
    Stream #0.2: Video: mpeg2video, yuv420p, 1280x720 [PAR 1:1 DAR 16:9], 20000
kb/s, 75.39 fps, 59.94 tbr, 1k tbn, 119.88 tbc
[mpegts @ 0214c060] muxrate VBR, pcr every 5 pkts, sdt every 200, pat/pmt every
40 pkts
Output #0, mpegts, to 'E:\Serviio\transcoding-temp-17901-MPEG2TS.stf':
  Metadata:
    DVR Index Granularity: 500
    WM/SubTitle     :
    WM/SubTitleDescription: Starr is surprised at her father's support for James
; Cristian learns Layla and Steffen slept together; Shaun agrees to help Darren
win Destiny back.
    genre           : Soap Opera,Series
    WM/MediaCredits : Erika Slezak/Robin Strasser/Trevor St. John/Michael Easton
/Robert S. Woods/Kassie DePaiva/Kristen Alderson/Melissa Archer/John-Paul Lavois
ier/Brandon Buddy/Bree Williamson/David Fumero/Kamar de los Reyes/John Brotherto
n/Farah Fath/BethAnn Bonner/Kathy Brier/Jerry ver Dorn/David Chisum/Catherine Hi
ckland;;;
    WM/ParentalRating: TV-PG
    WM/ParentalRatingReason:
    WM/ProviderRating:
    WM/OriginalReleaseTime: 0001-01-01T00:00:00.0000000-08:00
    WM/MediaStationCallSign: KGODT-DT
    WM/MediaStationName: KGODT (KGO-DT)
    WM/MediaNetworkAffiliation: ABC Affiliate
    WM/MediaOriginalChannel: 2807
    WM/MediaOriginalBroadcastDateTime: 2011-01-24T00:00:00.0000000-08:00
    WM/WMRVServiceID: ATSC-KGODT-80-7
    WM/WMRVProgramID: OFlpbHv+0T2uMT0iw7jF5g==
    WM/MediaOriginalRunTime: 1640261
    WM/WMRVEncodeTime: 1844674
    WM/MediaIsStereo: 1
    WM/VideoClosedCaptioning: 1
    WM/MediaIsRepeat: 0
    WM/MediaIsLive  : 0
    WM/MediaIsTape  : 0
    WM/MediaIsDelay : 0
    WM/MediaIsSubtitled: 0
    WM/MediaIsPremiere: 0
    WM/MediaIsFinale: 0
    WM/MediaIsSAP   : 0
    WM/WMRVRequestID: 98
    WM/WMRVScheduleItemID: 186
    WM/WMRVQuality  : 3
    WM/WMRVOriginalSoftPrePadding: 0
    WM/WMRVOriginalSoftPostPadding: 180
    WM/WMRVActualSoftPrePadding: 0
    WM/WMRVHardPrePadding: 0
    WM/Provider     : Zap2it
    WM/ProviderCopyright: © 2011 Microsoft Corporation. All Rights Reserved. Te
rms of Service: 
http://go.microsoft.com/fwlink/?LinkId=8430    WM/WMRVEndTime  : 1844674
    WM/WMRVExpirationDate: 1844674
    WM/WMRVBitrate  : 0
    WM/WMRVKeepUntil: 184
    WM/WMRVHardPostPadding: 0
    WM/WMRVActualSoftPostPadding: 180
    WM/WMRVContentProtectedPercent: 0
    WM/WMRVInBandRatingSystem: 255
    WM/WMRVInBandRatingLevel: 255
    WM/WMRVInBandRatingAttributes: 0
    WM/WMRVWatched  : 0
    WM/WMRVATSCContent: 1
    WM/WMRVDTVContent: 1
    WM/WMRVHDContent: 0
    WM/WMRVContentProtected: 0
    WMFSDKVersion   : 11.0.5721.5275
    WMFSDKNeeded    : 0.0.0.0000
    VBR Peak        : 159
    IsVBR           : 1
    title           : One Life to Live
    artist          :
    copyright       :
    comment         :
    encoder         : Lavf52.92.0
    Stream #0.0: Video: mpeg2video, yuv420p, 1280x720 [PAR 1:1 DAR 16:9], q=2-31
, 20000 kb/s, 90k tbn, 59.94 tbc
    Stream #0.1: Audio: ac3, 48000 Hz, 5.1, 384 kb/s
Stream mapping:
  Stream #0.2 -> #0.0
  Stream #0.1 -> #0.1
Press [q] to stop encoding
[mpegts @ 0214c060] st:0 error, non monotone timestamps 99000 >= 95940
[mpegts @ 0214c060] st:0 error, pts < dts
av_interleaved_write_frame(): Operation not permitted
C:\Program Files\Serviio\lib>
Now if I replace -copy    by     mpeg2video -sameq -r 59.94 -g 15
the file transcodes fine.
So I replaced the instruction in the profile by
			<Video targetContainer="mpegts" targetACodec="ac3" targetVCodec="mpeg2video" forceVTranscoding="true">
				<Matches container="asf" />
			</Video>
And then ffmpeg does not use -copy but specifies mpeg2video and the transcoding works