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Timeout Errors in MySQL

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Timeout Errors in MySQL
Hi:

I have a MySQL install on the same box as two Links and Two Forum installs. MySQL also serves up ads for an ad server on a seperate box. I am getting a substancial amount (5%) of timeout erros, but only on a couple of the installs (the "comics" install mainly). MySQL error log:

040621 7:51:50 Aborted connection 2893 to db: 'comics' user: 'cartoon' host: `localhost' (Got timeout reading communication packets)
040621 8:06:13 Aborted connection 2959 to db: 'comics' user: 'cartoon' host: `localhost' (Got timeout reading communication packets)
040621 8:08:42 Aborted connection 2964 to db: 'comics' user: 'cartoon' host: `localhost' (Got timeout reading communication packets)
040621 8:22:03 Aborted connection 2976 to db: 'comics' user: 'cartoon' host: `localhost' (Got timeout reading communication packets)

I read through some of the error info on the MySQL site, but have not been able to get the timeout error lower. I upped the timeout, and did some other messing around, no real change...

I have noticed the errors do not seem to start until 2-3 hours after the MySQL server is restarted.... then they seem to come pretty regularly. I think the strange thing is that the "comics" install gets these fairly regularly, yet the "cartoon" install NEVER gets them. Since the same Apache server serves both sites, they both have the same config on the Apache end as far as timeouts and such...

So, does anyone have any idea where I can go from here to try and get these errors lessened? Short of restarting MySQL every two hours, that is?
dave

Big Cartoon DataBase
Big Comic Book DataBase