TS Packet editor is great, seems to be exactly what i wanted. I've just been using the +1/+10 buttons to find the right positions, setting then hitting edit, done one and theres sound from the ads leaking in so i'm going to do it one or two frames further back.

edit: im getting a wierd problem where it goes all blocky and into a loop on video, but audio continues at the join of two segments. If you skip past the part at the end of the first segment and go straight to hte next it doesnt happen.
Also i'm using -f/+f to fine tune the start/end points, but sometimes it'll go a frame from the ad to a frame from the program, back to the frame of the ad and then the program continues.

When i click scan i get this:
Scanning File...
PID 0x0020 Continuity Error found at offset 0
PID 0x0000 Continuity Error found at offset 18988
PID 0x0030 Continuity Error found at offset 127464
PID 0x0041 Continuity Error found at offset 130284
PID 0x0040 Continuity Error found at offset 141188
PID 0x0030 Continuity Error found at offset 417747280
PID 0x0041 Continuity Error found at offset 417747468
PID 0x0040 Continuity Error found at offset 417758560
PID 0x0041 Continuity Error found at offset 829701716
PID 0x0040 Continuity Error found at offset 829712620
PID 0x0041 Continuity Error found at offset 1241901116
PID 0x0030 Continuity Error found at offset 1241901304
PID 0x0040 Continuity Error found at offset 1241910704
PID 0x0030 Continuity Error found at offset 1367281888
PID 0x0041 Continuity Error found at offset 1367285272
PID 0x0030 Continuity Error found at offset 1653851416
PID 0x0040 Continuity Error found at offset 1653865140
PID 0x0030 Continuity Error found at offset 1678636960
PID 0x0030 Continuity Error found at offset 1737731564
PID 0x0030 Continuity Error found at offset 1737731752
PID 0x0030 Continuity Error found at offset 1754655512
PID 0x0030 Continuity Error found at offset 1763398640
PID 0x0041 Continuity Error found at offset 1763402964
PID 0x0030 Continuity Error found at offset 1791926700
PID 0x0030 Continuity Error found at offset 1836836140
PID 0x0030 Continuity Error found at offset 1865967492
PID 0x0030 Continuity Error found at offset 1873134804
PID 0x0030 Continuity Error found at offset 1902370308
PID 0x0030 Continuity Error found at offset 1902370496
PID 0x0041 Continuity Error found at offset 1902375948
PID 0x0030 Continuity Error found at offset 1917593232
PID 0x0030 Continuity Error found at offset 1938171712
PID 0x0030 Continuity Error found at offset 2058197116
PID 0x0041 Continuity Error found at offset 2058201440
PID 0x0030 Continuity Error found at offset 2061649172
PID 0x0041 Continuity Error found at offset 2061654060
PID 0x0041 Continuity Error found at offset 2065794948
PID 0x0040 Continuity Error found at offset 2065797392
PID 0x0030 Continuity Error found at offset 2281271336
PID 0x0030 Continuity Error found at offset 2296782276
PID 0x0030 Continuity Error found at offset 2296782464
PID 0x0030 Continuity Error found at offset 2313116280
PID 0x0030 Continuity Error found at offset 2313116468
PID 0x0030 Continuity Error found at offset 2341094628
PID 0x0041 Continuity Error found at offset 2341098388
PID 0x0030 Continuity Error found at offset 2446330260
PID 0x0030 Continuity Error found at offset 2446330636
PID 0x0030 Continuity Error found at offset 2446330824
PID 0x0030 Continuity Error found at offset 2469471556
PID 0x0040 Continuity Error found at offset 2469493176
PID 0x0030 Continuity Error found at offset 2496510468
PID 0x0030 Continuity Error found at offset 2496510656
PID 0x0041 Continuity Error found at offset 2496515168
PID 0x0030 Continuity Error found at offset 2553055040
PID 0x0040 Continuity Error found at offset 2553072524
PID 0x0030 Continuity Error found at offset 2743957384
PID 0x0041 Continuity Error found at offset 2743961708
PID 0x0030 Continuity Error found at offset 2771334884
PID 0x0041 Continuity Error found at offset 2771339020
PID 0x0030 Continuity Error found at offset 2822296608
PID 0x0041 Continuity Error found at offset 2822301120
PID 0x0030 Continuity Error found at offset 2836728052
PID 0x0041 Continuity Error found at offset 2836732188
PID 0x0040 Continuity Error found at offset 2836746100
PID 0x0030 Continuity Error found at offset 2844348068
PID 0x0030 Continuity Error found at offset 2890464656
PID 0x0040 Continuity Error found at offset 2890470108
PID 0x0030 Continuity Error found at offset 2890918112
PID 0x0041 Continuity Error found at offset 2890921496
PID 0x0030 Continuity Error found at offset 2967599176
PID 0x0030 Continuity Error found at offset 2967599364
PID 0x0041 Continuity Error found at offset 2967603500
PID 0x0030 Continuity Error found at offset 2995780376
PID 0x0030 Continuity Error found at offset 3104075708
PID 0x0030 Continuity Error found at offset 3104076272
PID 0x0030 Continuity Error found at offset 3119570480
PID 0x0040 Continuity Error found at offset 3119589656
PID 0x0030 Continuity Error found at offset 3164333844
PID 0x0041 Continuity Error found at offset 3174172072
PID 0x0030 Continuity Error found at offset 3235274328

PID List:
Found PID: 0000: PAT Ver: 1 TS ID: 0x0004
Found PID: 0020: Program : 137
Found PID: 0030: H.264/AVC Video (as defined in ITU-T Rec. H.264 | ISO/IEC 14496-10 Video)
Found PID: 0041: ITU-T Rec. H.222.0 | ISO/IEC 13818-1 PES packets containing private data
Found PID: 0040: ISO/IEC 14496-3 Audio with the LATM transport syntax as defined in ISO/IEC 14496-3/AMD-1

Continuity Errors: 80, Transport Error Indicator Errors: 0

Scan Complete.
Time Taken: 30.20 secs


And it adds a bunch of listings of where to cut, what do i do?