I ran into another weird bug. I can't explain what made it. I just loaded the job and tried to nest. I played with CN 5.54 too but the same thing happened. It does nest on the good old CN5.48 though with no problem. I am attaching a print screen so you can take a look at the exact error text. Let me know if I can help with anything else.
P.S. It seem that I am getting into the habit of posting on late Fridays when no one can help me. Damn my luck.
I isolated the problem to Cab #1 ( U02 U 47 1-4x 53x 23 3-4). If you load it with ShopBot or probably CN5.48 it will miss nesting a partition for the same cabinet. On CN5.56 it will show that partition with completely messed up sizes for Width and Height. Anyways it seems the bug was caused by eCabinets. I re-did the cabinet and it nested correct with no errors even on CN5.56. I am still attaching esj file of the problematic cabinet for your review if such is intended.