That is a large number of modules that you require to be "thread-safe". Threads get an exact copy of the parent thread at the time of creation, and if for some reason (and it usually happens) a thread dosn't clean itself up completely, it will hang around wasting memory, which then gets incorporated into the next thread. Since you are not sharing data between threads in realtime, and apparently logging to a file, you could easily switch to a forked solution and save all the hassles you are experiencing with threads.
I would be particularly worried about the thread-safety of Net-SFTP, a quick google for "Net::SFTP thread safety" indicates it is not safe for thread usage.
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