I'm using the original core from Dennis. The fragmentation comes from my frequent file changes during testing. These are done at the PC where I store all files. I have been testing several cores, kickstarts and games (of curse...) without reformatting the card in between.
As I can see that could be the reason to the bad behavior of the blue board. When using the Yaqube ARM-board and boot it up with a hardfile, there are no issues (so far). The AIBB tests seems to run fine.