Just to tag along to PJ's post, remeber that PID and CKR are strickly "key management" terms and have no effect on the mechanics of encryption.
PID - Physical ID management - KVL-3000 ASN mode - ("slot 0, 1, 2....") - (L.I.D. FFFF, key data ABC123.........)
CKR - Common Key Reference management - KVL-3000 ASTRO25 mode - (CKR00001, CKR00002,......) - (K.I.D. FFFF, key data ABC123......)
While incompatible PID/CKR setting between a radio and keyloader will prevent a key from loading into a radio, it will not prevent one radio with one setting from talking to another with a different setting. BUT, the key ID and key data have to match or the radio will not unmute (and if it does you'll hear aliens

).
Here's a link to a pretty detailed, but HELLA long post that laid all this out pretty well. Check about half way down, you'll see a post from "515". He explained it pretty close to what I would so I'll save myself the typing.
http://batboard.batlabs.com/viewtopic.p ... 75&start=0
What I was going to ask, are you running analog or digital channels? Were your Spectras working before the upgrade, or did you upgrade because you acquired the Spectras and the upgrade would allow you to key them? Have you tried testing with a handheld, removing encryption altogether and verifying that your Specta and handheld will talk to each other in the clear based on your current personality settings? When you rekeyed the handheld and the Spectra, that'd also give you a chance to see if rekeying all the handhelds with the upgraded DX fixes your problem.
If you just read that and said "NO S**T SHERLOCK"... Then I certainly apologize, but I've caught myself missing some really basic stuff in the past so it never hurts to ask. Take it easy....