Basically, the issue is that chdir changes the current working directory, but that is global to the process, not to a thread. The result is that if anything else does a chdir, you will no longer be in the directory you thought you were in.

For the most part, as long as all of your scripts chdir to the same place you should be okay. You can probably assume that Apache 2 and mod_perl 2 will not do any chdir stuff, but other CPAN modules might. Best to test with high currency and see what happens, as well as grep'ing any modules you use for chdir.