my debug statements (removed for readability) showed the script going all the way back to the select statement and then never coming back,

It ought to be fairly easy to tell if the timeout is failing to trigger. Just bracket the select line with

warn "before select: " . time;
select...
warn "after select: " . time;
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And if it is, then that to me indicates that something is very broken. But I don;t know enough about it to say what.

I'd suggest that you confirm your suspicion, and then post a new SoPW with "select timeout failng on Ubunto vxxx & Perl vx.x.x". With as much logging from the period immediately preceding the failure--perhaps a tcp trace--as you can gather.