Suspect as always is tranients on I/O pins that inject charge into the
substrate, and potentially corrupt FLASH cells. Or transients on Vdd
that exceed gate ox breakdown. Best way of detecting a condition like
this is a DSO set to trigger on something like this -
Vss - .7V > Vtrig > Vdd + .7V
and look at key interface pins talking to loads than can generate
transients, like a relay, a MOSFET driving a relay (transient feedback
thru Cgd). Set up jig to cycle power, and enable DSO on signal that
triggers power up and down.
This is vary tedious to find, patience is a virtue.
Also in general power supply sequencing, make sure PSOC comes up
before any I/O loads do. If you cannot guarentee that make sure all pins
clamped by zener arrays, avaialable from On Semi, Vishay, Fairchild to
name a few.
How do you find the PC corrupted?
Would there be some cases where your EEPROM value is out of your expected range and your program perform not as you expected?