Perhaps you could give us an example of this "weird problem", an explanation of the "preferred output" and how it differs when your script is converted to an exe. Are there any differences in the setup of the machine running Perl and the machine you run the executable on which may be a contributing factor in the differing output? Or dependencies external to your Perl script that exist in one but not the other?

Update: If nobody here can help you, you may want to try IndigoSTAR support, but I suspect they will also ask you for an example of what is not working the way you expect it to.

Martin