Then, I would suggest rethinking your design, if you can. e.g., I hear about POE, perhaps that would be a better way to design to make it easier to debug.

Even without POE, you could do all this on a single thread using IO::Select. Especially if there's only one CPU anyway, having multiple threads isn't going to make your program go (much) faster. It will be a battle between the overhead of task switching in the kernel (far removed from your app) and the optimisation of that task switching. Otherwise, selecting on your hundred ports will probably be faster and easier to write.

A distinct possibility in your current problem is that this thread is chewing up so much CPU time that the OS starts to throttle it, and outright ignore it. Try inserting a "sleep(1)" in your loop so that it only checks once per second, rather than as often as the CPU (and OS) allows. Or, better yet, calculate the time difference between now and the desired time, and sleep for that long - which will use zero CPU time until the desired time.