My question is whether CPAN.pm had anything to do with it, or did something else happen on my system (like a Fedora update over the weekend, for example) to cause the weird behavior.

I don't know about you, but if I use CPAN on Friday, and over the weekend an upgrade of my OS might have happened, and on Monday, my system is acting up, my (non-root) use of CPAN wouldn't be the first thing I'd consider as the cause of the problems.

Having said that, I always run CPAN with a dedicated user (often called 'cpan' or the uninspiring 'perladmin'). The worse it can do is silently replacing files in site_lib with Trojans, but that shouldn't effect tcsh.