Hi Richard/Harel,
This isn't something I've come across really, but I've not done rigorous benchmarks (yet). So far I've not had too many problems with v5, but I guess it depends on your app. (I'm only using MySQL5 live for a few smallish apps so far)
This should be of interest if you've not seen it before:
http://www.mysqlperformanceblog.com/files/presentations/UC2006-MySQL-5.0-vs-4.1.pdf
In particular look at the slide which covers group commit as that's where one of the biggest performance degradations seems to be.
I'd be very interested to see your particular cases it's much slower - I'm planning to migrate a pretty big server from 4.1->5.0 and it'll save me a lot of time tracking down any problems I'm sure. :)
It's also possible that someone here can suggest fixes/reasons for the differences if you can provide more detail.
Cheers,
Toasty
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email: 'toasty'*3 at gmail