Personally, I would recommend looking at Filter::Simple instead of Filter::Util::Call, as Filter::Simple at least provides a simpler (indeed!) interface to source filters.
But, as you don't show any code we could look at, it is quite hard to tell you what is wrong with your code, or mod_perl2, or how the two interact. My guess is that you have problems with the different Apache backends. For example, I can easily imagine Apache threads not playing well with a source-filtered Perl script, especially when trying to reload.