To answer this specific question, this is a limitation of the SG-8 firmware. The firmware in the 440/450 code had a similar issue at one time. At runtime, the SG-8 actually MODIFIES the ladder memory, one of which was a hidden parameter in the SG instruction. Hence, we would download a 0 for this hidden parm, but then the PLC would change it (at PGM->RUN transition) to something other than 0. Then, when we uploaded it, it "does not match" the hidden parm, hence the "differences".
If you look at the details dialog for the differences, it should be on SG instructions, one with a parameter value of K0 on disk and one with a non-zero value on the PLC side.