I had a similar issue going to tape with 720p25 to digital beta. I never figured what the problem was, as it was intermittent. On some tapes I was half a frame late, then I would be fine for the rest. I was largely working on G5s and figured it may be due to the down conversion. I couldn't get any information from Aja tech support on this, as the only documented issue is that you will be off by 1 frame on up/down conversions.
You can try to offset it under audio video settings and adjusting the offset in device controls. See if you get any love from it.
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