It sounds like the module isn't included, and hence isn't used properly at app runtime. It's probably dynamically loaded in a way that PerlApp has problems detecting when deciding which modules to bring along at build time.
The canonical way to solve that problem is to explicitly "use" the module somewhere in your script (preferrably with a little note about PerlApp acting up). But from "IO::Select module is being added at compile time" I take it that you already do that.
What if you "add" or "bind" the file manually with a command line option?
perlapp -h for syntax.