How fatal is the maximum execution timeout warning in MySQL
DCoder answer is good, try to change the maximium execution time in MySQL server, also, you can try to find what query is making the noise using the slow-query-log (you can activate it and is very useful in the case of messy querys).
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If you're using MySQL on windows environments, I strongly suggest to put it on a linux server, because it's lots slower over windows.
About your concern, There is no real danger about your data, and changing the slow-query-log option or maximum-execution-time option doesn't compromise the databases... but do some backup before change anything, just for extra security.