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wallet.dat
wallet.dat.rewrite SHOULD be automatically removed as part of the upgrade-to-0.5 process; I don't know why it isn't in some cases-- and, frankly, I would much rather spend time getting really, truly secure wallet solutions working.
RE: bitcoin version 0.4 starting up on your machine:
You should run the old bitcoin, un-check the "start on windows system startup", then exit.
Then remove it using the Add/Remove Programs control panel doo-hickey (did that move again in Vista?). You should see both "bitcoin" (the old 0.4) and "bitcoin-qt" (the new 0.5).
... all of which is, I know, annoying and painful. Again, frankly, I'm more interested in spending time on the very-highest-priority issues rather than making every beta release upgrade completely smooth in all cases.