Go delete the plugins that you mistakenly copied from a previous version of Photoshop, or disable the additional plugins folder that you mistakenly pointed to the plugins from a previous version of Photoshop.
Copying plugins from an older version is going to cause conflicts, as you just saw.
All of the plug-ins were first uninstalled and then freshly installed. So copying plug-ins wouldn't seem to be the problem since none were copied. One thing I did as in experiment was to simply open a file in Photoshop CS6 Beta; then without doing anything to the file, open Save As and try to save it as a TIFF. It still created (and creates) a pdm file. My work around is to simply create a PSD file with Save As. If that PSD file is brought back to LR4.1 RC, I can Export it to CS6 and Save it (not Save As) and I will end up with a TIFF file back in LR. There are no problems with Save; only with Save As. (Actually, the PSD file is just fine with me.)
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Jack, the Photoshop CS6 beta does not have a basic problem of mixing up file types.
The problem pretty much HAS to come from Photoshop CS6 enumerating the file format plug-ins from another version of Photoshop. Go look again.
Or go look at the Photoshop System Info dialog, and see where the duplicate plugin is coming from.
Either you copied the plugins into CS6, or you use the additional plugins folder preference.
Duplicated plugins from a previous version are the known cause of the file type menu getting out of sync in the save dialog.
Somewhere, you do have duplicated file format plugins.