Are you having the "Allow only one project open at a time"?
If not, many projects may be open - and question to save may refer to one not in front of you.
I noticed that just changing parameters in plugins does not make project dirty. And which location on drives are holding projects?
Nothing under \Program files, or?
Thinking of authorization to save.
And if external usb drive, power saving options may kick in and it's not available when saving.
Never allow power managing to kick in, see to that it's not allowed in device settings.
How many saves do you have on project, it should be a backup for each save?
From timestamps you should be able to tell a little more about what happend.
It could be the new save is done in another location from opened project.You may be looking in the wrong place.
Just a bunch of things that may inflict in your case...