MPEG-PS and PCR issues I think. I'm more familiar with MPEG-TS though, and it continues to astound me that Avatar Music Video coordinators don't refuse anything that isn't MKV to be honest.
Is there any reason you can't just submit it in a different format? Either MPEG-TS or MKV should work fine. In regards to your actual problem, can you try in TMPGEnc with a higher frequency of I-frames? What is probably happening is that PCR packets (timecode info based off a core system clock) are not frequent enough in your stream so dshow is having issues with frame accurate seeking. lavf is more forgiving with such things and will scan or index the file if it cannot find a PCR right away, making it slower but more accurate. Of course this isn't an issue in modern PC hardware but dshow isn't exactly a recent thing.
If you MUST have mpg format, you can try remuxing with avconv and it may fix it or re-index it for you, worth a try I think. MPEG-PS is meant to have it's own timecode setup but because it's H.222 it still does this via PCR with a fixed base clock instead of the sexy way m2ts does it with dedicated timecodes. Still worth trying TMPGEnc with more I-frames or other similar flags tweaked to provide more seek info for the GOP. Maybe use avprobe to check how many I-frames are in your content between different encoders even as it could just be you don't have enough GOPs rather than the PCR being infrequent. So a few options on how to progress there.
glhf~
