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
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Categories are tied to the relative path of the associated app. When you rename them, they're considered a different app and the default category returns.
Incidentally, you shouldn't rename your app's directories at all as it will break detection by the automatic updater.
Sometimes, the impossible can become possible, if you're awesome!
There is an error in LibreOffice related to a long path name, and the temporary get around solution was to reduce the size of the path name. (as in the forum for LibreOffice).
L.A. Cole
The workaround was to move your font files: https://portableapps.com/node/34258#comment-198150
That fixes the crash, too. It's been fixed in the base package already. We're just waiting for the publisher to post it: https://portableapps.com/development/outdated
Sometimes, the impossible can become possible, if you're awesome!