I finally figured out why putty drops my connection (even in the middle of typing in a command) and thought I'd share this.
In putty configuration;
go to connection/SSH and click on "Kex" under "Options controlling key re-exchange" change the "Max minutes before rekey" to "0" and the timeouts should stop. (You can set the Max data before rekey to 0 also if you prefer but I left it at the default)
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