I noticed that when I installed the new Smart String Utility software that I was (for a while) running the OLD version and didn't know it.
So I started going to the Smart String thread, then picking RJ' sticky thread on the mod, and then downloading and running it straight from there. I later removed the old version manually, because the shortcut on my desktop was for the OLD version, not the new. I then put the new .exe on my desktop to I knew it was the correct one.
Just a guess, but make sure its the correct software.
I also did an ERASE first, then reprogrammed my PIC(s) after that ... using a pickit2.
For me, I modded about 13 controllers from v1 to v3 and they all work great.
Also make sure the wire order on the SSC matches the type of SS item your using. I have what I thought was a couple of bad SSCs ... but they were setup to work on one variety and not the other. The wire color from last year to this year only add to all the confusion.