Junior, first, there are actually 2 problems you're having here, and second, I think at least half of what you describe (the GUID issue) is completely different - probably belonging in a new thread (or call).
My guess is they resolved it.
Problem 1: Duplicate GUID's
Depending on how you're performing your imaging process (which we don't know yet) you may be running into a problem we had with another customer where, once in production, the system is not recognized and gets a new GUID. We don't know for sure why the systems are not recognized post imaging when, about 99% of the time they are, but we know it happens.
To resolve this, we're working on putting the GUID into the deployed image while still in automation. One of our customers was able to do this and completely removed the duplicate GUID issue.
Problem 2: Generic Naming (Win??? name)
This is a bit different from your system name. The Win-??? name is a generic name generated by MiniSetup if you either 1) have an * in for the computer name in the unattend file or 2) have that section of your unattend file misconfigured and therefore ignored/skipped/whatever by MiniSetup.
Regardless of the name though, we SHOULD recognize the computer. We SHOULD see that it's the same computer based on MAC / UUID hash (called uniqueID in our console). If we don't, you would see the duplicate GUID.
The name does not affect the GUID (well, shouldn't, but might) and the GUID doesn't affect the name.