I also have an HVR-1500 (not the the 1500A). I am using a Blackmagic Deck Link Extreme.
I get the exact same error messages that you do anytime I try to batch capture with FCP. Sometimes it captures clips and the time code is off by 2-3 SECONDS. Other times it gives me a TC error message and stops cueing. I believe I have tried every possible menu setting in the HVR-1500 operational menus. I have all the latest software updates for FCP and Blackmagic.
However – if I use the stand alone Blackmagic Deck Control software the HVR-1500 captures footage accurately and without any problems 100% of the time. It works PERFECTLY – just like my BetaSP 1800, a Digital Betacam deck, or a DVCPro HD deck.
My theory is that the FCP software is not able to accurately control this deck during cue-up. It somehow loses communication with the deck’s time code. I have spoken with two different Sony broadcast engineers, and one Blackmagic tech support person. They all acted like they had never heard of the problem, but the Blackmagic support person is the one who told me to try the Blackmagic Deck Control program. I have not spoken with anybody at Apple (yet) because they want to charge me $$$ just to talk to them about a bug with their software!
I am also going to post this info/question in the HDV and FCP forum to see what kind of response I can get.