Before delving into the issue itself I found rather ironic and sad fact that I could not login into this forum from my PFF and had to use IE 
just for this.
Now to the meat of it: For the past few days I realized (hard way) that my bookmarks are not being saved. I'd make all the changes, they all show up while either looking at bookmarks directly, or using bookmarks manager. Everything is fine until I close the application (v.1.5.0.7). Once I go back the changes are mostly gone, some, earlier are there, but most are gone - can't figure the pattern.
So, apparently there is some delay when the bookmarks are saved? Or PFF just rolls back for some reason?
Could not find similar topic in the forum before.
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of FFP? Or maybe you have to do a reinstall of the program if your program got corrupted.
When you say "some earlier" are there, do you mean that, 1. you did some changes, closed FFP and and opened it up, and some of the bookmarks remained? Or 2. that when you did changes, then closed, then opened, all the changes were gone? Or 3. You did changes, then closed, then opened, saw your changes, then closed and then opened a 2nd time and the changes were gone?
With 1. It seems like you didn't bookmark it properly, though I don't see how the process can get messed up. (ie Not your fault)
With 2. It seems like it's not writing the the bookmarks file, like it's been moved.
With 3. It sounds like you may have different profiles being written to.
Don't be an uberPr∅. They are stinky.
It's not a clean install, it's Portable, and version 1.5 I've been using for years now.
Now, the problem seems that bookmarks file is not getting updated/saved even though from within the application it shows the changes. Probably, corresponds to #2 of your scenarios.
Perhaps, or at least now is the issue, it is not saving when one page of multiple tabs open is attempted to be saved in existing folder in bookmarks.
For example, I have folder in Bookmarks called "Friday" and currently have Tabs 1 - 12 open and go to tab #8 and click "Bookmarks"-"Bookmark this Page" and select that existing folder it shows all fine, but timestamp of the file does not change. It was saving/changing today before, and no I did not close the application since.