I would say that might have to do with id's and how the iso was built...additionally this linux cd might be depending on certain memory locations of either a soft modded or hard modded ps2 that are not present in the ps3 bc emulator...
Personally I would just install linux on the ps3 part of the machine if you really want this ability I imagine it would be very slow through the emulator...
Though if you have a mind to I would start looking at ps2 images and compare to the linux live ps2 disc. I would imagine that if you might have to do some repacking possibly...
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The thing is im on cobra cfw so installing linux on my ps3 is out of the question for now...... As for rebuilding the live linux ps2 iso... I wouldnt know how to do that.