JabRef saves changes, but not to Bibfile, which stays unchanged

I updated from JabRef 4.0 to 4.3.1 (I deleted the old version beforehand). In the process, I updated my Java to 181. I did this yesterday on two different computers, both running Windows 8 (x64).

I now have the problem that when I add new entries to the .bib-file I am working on, and save it, the “last modified”-date does not change in file explorer. When I try to compile my LaTeX-document with the bibliography, the entries that were added since the update are not included.
When I open the bib-file using TeXworks and search for the new entries, they are not there.
However, when I close JabRef and then open it again by clicking on the bib-file, the newly added entries are again perfectly listed in the list of entries in JabRef’s UI. So, everything new is saved somewhere, but seemingly not in the bib-file where it belongs.

That sounds really strange. JabRef only shows you the entries it finds in the bib file, nothing more (and hopefully not less). So my initial guess is that you somehow made a copy of your library. JabRef is editing one of them, while latex uses the other. Thus, please make sure that the complete path of the file is correct.

If this does not resolve the issue you can also look for a .sav or .bak file with the same name as your library. These files are backups that JabRef creates. If such files exists, can you please look if they contain the new entries.

Thank you.
I made sure that the path is correct, loading the bib-file from the path multiple times, and using “save as” to save the version that, according to JabRef, should contain the new entries, in the same folder, with the same name, to overwrite.

Interestingly, within the “save as” dialog, the “last modified” (of the bib-file I am having this issue with) that I can see in the explorer window is the actual time at which I last saved it. Then I choose to overwrite. But in Windows Explorer, it is still an unchanged “last modified”-time, with the above problem.

There are no .bib.bak or .bib.sav files in the folder (hidden items are visible, so I am sure that nothing else is in the folder).

I also replicated the problem with Antivirus turned off.

I just ran JabRef as Administrator. Then this happened.

Any changed I had made, as described above, were lost. However, I could make new changes, and save the file, and the file would save perfectly, including a .bib.bak-file simultaneously.
I would then close JabRef. Then, when opening JabRef again, but normally, without administrator privileges, I would again face the bib file with all the changes I made over the last day, but not those changes I made as an admin. Again, any change and saving now would not display the file as having been changed in the file explorer.

So, I seem to have the correct functionality of JabRef only when using it as an Administrator, and when I do not do so, it still somehow saves my changes, but I am unable to see where, and how, and access them.

The two files exist in parallel; I just experimented a little, and any entry I create with/without admin rights will be visible after I save, close, and open the file again with/without admin rights; the changes I make as an admin and save are saved as expected, and the changes I do not make as an admin are also registered, but not visibly to me in any file in the directory.

This really sounds like you have two copies of library in two different folders (maybe one in All Users (only accessible when you are admin) and the other one in your personal folder). When you chose “Save as” (in JabRef started without admin rights), look at the complete path where you save the file to. I would bet that there is a difference to the case when you start JabRef with admin rights.