Solved this morning by just restoring just ONE XML FILE from a Ghost image backup. If this happens to anyone else on XP, here's what you can do (so long as you have a C drive backup or image from when it worked).

1. Be sure in XP you have "show hidden folders" enabled (folder options)

2. On the C drive, go to  this folder (full path below) and be sure [yourusername] is the user acct involved with your AA installation: It will vary depending on how your system is set up. If you have other versions of AA installed, it's real impt you navigate to the 5.0 folder in path below. (We have AA3.01 and CS5.5 on this system along with CS6 with patch)

C:\Documents and settings\[yourusername]\Application Data\Adobe\Audition\5.0\

3. Now find the file AudioPlugInManagerSettings.xml

4. Rename that file on your C drive to something like  AudioPlugInManagerSettings_OLD.xml (or whatever else you like)

5. Now restore the AudioPlugInManagerSettings.xml file from your backup or image to the same location above.

And, the Waves plugs are back in CS6.  How this XML file got corrupted in our case is beyond me, but looking at the XML text in the one on the C drive before fixing,  it had the Waveshell entries but not the actual Waves plug ins.  And despite deleting all plugs in CS6's plug in manager and rescanning as I posted above, the actual plug in DLLs  were not getting found (tried a few times as noted in orig. post). They were in a folder the plug in manager was pointed to - same way we have had them in CS5.5 for a long time (and CS6 too until suddenly they were gone)

So, in the end, did not have to restore the whole C drive, just the one XML file. Total fix time (once we figured this out!) - about 1 minute.    Don't know about other imaging programs, but for Ghost using XP, you can find the individual file easily with Backup Image Browser in Ghost and restore to original location directly from that.

Weird how only the Waves stuff got corrupted, yet deleting and re-installing all other plugs (UA, Izotope, others) worked fine repeatedly each time we tried. Each time CS6 found all of them. It always found the Waveshells and enumerated numerous "parts" of those shells each time it ran, but never found the plugs themselves. Funny, given the shells are in same folder as the actual plug in DLLs are.

Anyhow, hope this helps others.  Back to audio work here!

Thx Steve-- I somewhat suspected that might be the case, but tried what I posted first and it worked so stuck with it! My concern was whether Audition would have then dropped some of its own "native" and Adobe licensed plugs, good to know that it would not from your note though!

Hard to figure how that XML got trashed in first place,  though. 

You're right. I'll try that too and send him a donation, which should do anyway for all the work he's put in on so many things like SES2SESX etc. 

Oh well!! Guess I'll stick to using Ghost for now with it then, though Steve's "delete" thought also seems applicable if stuff like this happens again.  

And maybe SuiteSpot will at some point update AuditionFX. But he's done a huge amount for many AA users already with his other stuff, so no rush, he has been very giving to the AA community for a long time.