This should not occur with 6.1.0.1 unless the .threads file really did write out to zero size..
The slowness you're noticing is somewhat normal for the upgrade, for the time being, at least. I would advise asking your host to install PHP so you can take advantage of the UBB Accelerator...
Your board is pretty big - you might also want to consider moving to UBBThreads.
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Charles Capps
Programmer, Infopop Corporation
Please do not contact me privately for support - post on the board or open a support ticket instead!