I recently found out while trying to re-program the ipac in my decade old control panel on Win7 xp64, that it wouldn't work. I had the same issue as you with keys not programming to the ipac chip. Can't recall if the keypresses came out correct or not though. Anyhow, I needed to run the legacy software from an older OS. The new ipac software won't cut it on older ipacs.
So I leeched an older version from ultimarc's site, and ran it an an older laptop running Windows 98. Hooked up my ipac to that, and it reprogrammed like a charm first time out.
Can't promise you it'll fix your issue but the ultimarc legacy software available here....
http://www.ultimarc.com/download.html