NeonCube Problem

[PurpleMadness]

Hopefully im posting in the right section since im a little lost. Anyways i have a problem with NeonCube each time it patches it turns it into .file and changes anything that was inside the file to the number the patch was so for example. if i wanted to patch Me.bat and inside it was echo off and after patch it would just simply make Me.bat into Me.File and if u open it with notepad it would just say the number of the patch. SOMEONE PLEASE HELP