I tracked down the missing hardcoded registers and they seem to be set correctly, these are JPEG engine registers for control, mode, macro block size, etc, all seem correctly set. If they're set incorrectly the JPEG engine wont work at all. Then I realized that one of the EngDrvsOuts functions was'nt being hijacked logged correctly, and the calls did not go into by log. Oddly I can't hijack this address (function entry) but when I hijacked the next address it worked. So I logged all registers again and looked - but without any new result. This EngDrvsOuts function is only used in some rare cases with the jpeg engine.
So I'm, currently back to changing registers. I have gathered various bits of information regarding these, but nothing conclusive yet. I now need to investigate each registers that is used in conjunction with YUV image transfer in blocks into the JPEG engine, this is around 20 registers around 0xc0f11??? and 0xc0f13???.