I think the Superchips used EEPROM, which should have a data retention life of 10 years minimum if they were programmed correctly.
I think it's more likely that:
1. Your engine has aged a bit and there is some carbon buildup causing increased compression ratio.
2. Your fuel octane isn't what you think. There is a guy here in Colorado Springs with an octane test engine, he routinely tests the pump gas around town and finds it wanting for 2, or sometimes 3 points.
3. In the early 90's, I had several versions of SuperChips in my '89, all programmed by Peter Wales, president of SuperChips. None of them worked terribly well, some programs were awful (rev limit -vs- PIP filter issues), and all had too much timing advance.
You in St. Joe? I used to live outside Stevensville, had a duplex on Rocky Weed Road just west of Hollywood Road.