yeah, a reflash should pretty much have solved it
(a reflash without SD cards inserted during boot anyway .. the system will look for a bunch of things on SD as overrides .. but ejecting them and a flash solves _Everything_ pretty much
-- except for persistant nand problems or other weird stuff like that. Sounds like you've covered the bases ... hmm.
In your homedir, look for .mm (dot at the beginning) -- they're "hidden", like .desktop and .rc files and so on. Should be ~/.mmpref.conf as the full path.
Everything _else_ works fine though right? (ie: so no general corruption..)
I dunno .. something must've been tried and missed by mistake; try another reflash?
(*swallow* .. lame advice, but.. guessing
Starting okay from terminal, but not from boot; that would suggest a timing or environment issue ..
Well wait, you can't boot into minimenu ("switched to" minimenu) or do a gui change temporarily to minimenu (within session from xfce to minimenu) right? but you can launch it with startmmenu from terminal. (working through a touch.. if you can't boot into it, thats one thing.. something might not be ready yet for whatever reason.. but if you can't run it from a switch via the gui switcher from xfce, but can from terminal, then it is very likely the gui switcher gui,.conf ... but you've checked it.)
What about dos line endings or something? did you prepare a gui.conf from Windows and copy to SD and then into nand? (did you get permissions and ownership right?) Maybe you had D?OS line endings and borked it subtly but invisibly, though line endings likely wouldn't be a problem there anyway...
jeff