FWIW I'm running on a Buffalo Linkstation with Freelink, rather than a regular PC. Anyway, after much digging around with some help from a mate -- who admins mysql for a living -- we narrowed my problem down to mysql. Despite installing (and recommending, in other threads) version 5.0.45 we found that it would hang, randomly, on a particular query. The same query worked OK on a PC, so on the NAS we decided to downgrade mysql to 4.1 and since doing that everything seems to be fine. mysql 4.1 is also a lot lighter on resources! :)
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