I beleive this is not perl "decides" to load wrong perl58.dll, but rather OS find wrong perl58.dll within its search algorithm.
If you have a possibility to make existing perl58.dll to be further in PATH, then do so, although this could be impossible sometimes...

Also, if the problem exists as you describe, this is probably a chance to file a bug report to PerlApp support team
I do not know exact details of PerlApp, sorry...