XnView Software

When this is set:
Tools > Settings > Integration > Save settings > as INI file in folder: User (default)
Folder used for other files: User
then none of the settings, nor bookmarks, layout etc. are saved (if I exit XnView and open again, everything is set to default again).
no .ini file is created (at least not in home/ania)

If I set:
Save settings > as INI file in folder: XnView
Folder used for other files: XnView
then after closing and re-starting, XnView freezes immediately (or is so slow that it's not usable).
this time, an .ini file is created in the XnView folder .

With this setting:
Save settings > as INI file in folder: XnView
Folder used for other files: User
at least the settings from Tools > Settings are saved, but bookmarks aren't saved.

XUbuntu 9.04

I noticed this problem too. I was able to get settings to stick by setting everything the way I wanted and then clicking "ok" in the Options menu, and then going back into settings and reclicking OK again. For some reason, it won't stick if you make changes unless you go back in and click ok again without changing any options the second time. At least that worked for me.

So, to recap, after you've made the changes you want, you get them to stick by going Tools > Settings > OK. Don't do anything else at that point. If you do, then make sure you go back and reopen settings and click OK again without doing anything.

I was thinking about it, and after I did that I believe I also logged out and back in again. The program seems to need to create a setup file in your user account for settings to take hold and a reboot or logout/in might be required.