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A lot of advice given in various Mac sites appears to cargo cult style instruction. Running the file permissions checker. Backing up your home dir and then restoring it. Resetting the PMU and PRAM on a regular basis. All of this is done as a preventative measure even when they've not changed or installed anything. Invariably they don't know why they're doing it but they were told at some point to do so to fix a problem and therefore continue.

That would seem to be more of a hold over from pre-X days. Then most anything could be cured by deleting the preferences files. One or all. I found that true conflicts between pieces of software to be rare. Problems that were solved by clearing the PRAM, even more so.
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Glenn