First off, try running (a copy of) your code with the DBI stuff commented out. If your problem goes away, you know that's where to look.

Then, produce a cut down verion of your deamon script that only contains the DBI checks against a single, test installation of MySQL, and try to reproduce the problem by setting the frequency as high as you can.

At that point you should have a much smaller script that reproduces the problem much more quickly. If you then post that here, the DBI experts here (not me!), will be much more likely to take the time to review your shorter code and perhaps spot the problem or offer suggestions as to a way forward.

I have a vague recollection that by default (back at version 3.something), MySQL hung on to unclosed connections for something like 900 seconds? And that there was a configuration option (at the server end) to have connections timeout more quickly. My recollection may be wrong, and it probably wouldn't produce the symptoms you are seeing, but it the kind of thing that those with good MySQL experience may spot for you, once you have isolated the problem and posted a concise script that reproduces it.