Not exactly a Perl question, ;) but since I happen to know the problem ... here you are.
This page should give you the answer.
Shortly, if it is not a timeout problem, it could be that your query has exceeded the size limits set by "max_allowed_packet".
Check the queries that you are feeding the server through the DBI, and see if you have the same result in a command line client.
I also had this error when I tried to update a BLOB field with a chunk of data bigger than the field size.

I hope these hints could be helpful.
If none of the things listed in the manual are solving your problem, you may try at the MySQL mail list

update Try also this link. It will give you more than 200 comments on this issue.
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In reply to Re: My MySQL server has wanderlust... by gmax
in thread My MySQL server has wanderlust... by Sinister

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