This may not help unless a Roland tech reads. The Roland tech that looked at mine found an internal setting that was wrong. Where it read : 00000000, it should have been something like : 000000100. After he changed it it detected the registration marks and worked fine. I don't have the machine any more so I can't be of more help. Like I said a technician may know what this setting is.
I have no Idea whatsoever about the internal setting you describe.. however In my case, when my SC500 not reading the crop marks, I went to perform the calibration I outlined above and found the VR was damaged (ie: the screw head and wiper were completely missing!) - The voltage on the calibration readout was stuck at .02V (no where near the 2V it should be per the service manual). I replaced the cutter carriage board (had a good Variable resistor on it!) and calibrated the voltage to the 2V. and my sc500 reads the crop marks perfectly now, even through laminate.
I do recall reading a post somewhere on here about not putting the internal DIP Switch to the "SC500" mode, because someone was complaining that their SC500 failed to read crop marks when the DIP was switched out of CJ500 mode? Maybe thats what your tech was looking at... and candy could check that as well.
BTW: What Part of Mississauga are you from? My Uncle used to own Meadowvale Stables over in Brampton. Right there along side the Credit River/Meadowvale Conservation area on 2nd Line West. (they call 2nd line west "chincousey road" or something like that now - The farm, stables & house are all long gone now
-t