Possible causes:
1) It probably has nothing to do with your image files, but you won't know until someone else tests one of them. You could create a small 50% gray TIFF file with transparency and post it, assuming you know it exhibits the issue with IPP.
2) At the download link you provided:
http://www.russellbrown.com/scripts.html
There are two installers for Image Processor (CS5 and CS6). Did you download and install the CS6 Version Installer?
3) Another possible solution other than modifying the script is to reset the PS Preferences file. When strange things happen in PS with no explanation this usually fixes them. My PS CS6 was inflating all new files by 1.4MB. After examining one of the files it turned out PS was inserting a Costco printer profile into every new file. So don't automatically assume your PS image files are not somehow being corrupted and causing loss of transparency in IPP. Creating a new Preferences file resolved my issue:
http://forums.adobe.com/thread/375776
You may want to record your old Preferences settings prior to creating a new one, but test it first with the default settings.