I've checked support for this issue, but may have missed seeing it.
I have been using portable apps since version 1, and have current up-to-date apps on a Vista 64-bit home premium laptop.
I have both OpenOffice and LibreOffice installed, but I put LibreOffice in a new category calling it Office2. I did this several months ago, but because I was having issues with LibreOffice and long path name, I renamed the directory this weekend. My Office2 category disappeared, and LibreOffice went back to Office.
I was able to reproduce this. I created a category called File Managers, put file manager apps in the category. Renamed one of the directories and it went back to the original Utilities.
How can you get your categories to stick?
L. A. Cole