Nevermind, I got it
Double-checked all my permissions and it looks like a dir that needed to be at 777 wasn't. Got that changed and it seems to be working much better now.
Sorry for the trouble.
Might be a good idea to create a sticky post atop the troubleshooting forum that goes through all the different solutions to the not-indexing issue since it comes up so much...
(oh, and I meant mySQL 4.1.11 in case anyone got confused there)
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