Ok, hopefully this helps someone out but it seems to be working now. I did break the cardinal rule by changing two things at once, so I am not exactly sure which of the two was the magic ticket, but I have my suspicions...
Basically I did some more research on the Willem board, and found people setting their bios settings to EPP (mine was set to ECP). So basically I swapped out the parallel cable for a different and shorter one, and also changed the parallel port setting to EPP. One or both of those things enabled me to burn my eprom and have it validate correctly. Haven't tried putting it back in the A500 yet, but it is a big step in the right direction, and hopefully that helps someone else too.
I would say the EPP/ECP setting did the trick. ECP has issues leaving the strobe line in undetermined state or in some locked state so if you want to control it through software it causes problems. And worse of all, that's the default setting on most parallel ports.
I had other issues with programming SRAMs/EPROMs-- the power management screwing things up and i/o ports not being accessible due to some user access control protection crap in recent OSes.
