MySQL timeout counts even though script is running

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http://serverfault.com – I have 2 pairs of python scripts that run 24/7. 2 of them perform data insertions, 2 of them perform analysis. What happens is when I look at the connections in MySQL Workbench the 2 performing the insertions have time counters that never get reset to zero. The scripts performing the analysis are always on. The problem comes when this count reaches 28800 I get the "MySQL Server has gone away" error for the insertion scripts but never for the analysis ones. This seems very strange as the insertion scripts are running every 4-5 seconds. The analysis ones are just looped and run forever con (HowTos)