[snip]
>Check your mysql system variables for timeout variables (SHOW
>VARIABLES;)

Thanks Jay.  After I do this I see there are a number of timeout 
values,  none which refer to a sql command timeout.  Are you able to 
pinpont which value I need to manipulate?  Also, if I increase this 
value, what are the drawbacks of doing so (i.e. performance, etc.)
[/snip]

In the areas where we have increased timeouts we have not noticed any
degredation of performance. I am not sure which value you will need to
manipulate, as it has been a while since I have had to deal with it. A
visit here
http://dev.mysql.com/doc/mysql/en/Server_system_variables.html
might help 

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