Yes, I can reproduce something here, but the skinning engine appears to be getting very confused.....
This is what I did:
I started off at 100% size, Segoe UI 9pt.
Changes made to font size stuck correctly.
I then changed to 125% size, and started playing with the font size again.
Changes made here again stuck correctly.
I finally attempted to revert back to where I was, at which point things went pear shaped
Carrying on playing with it, I managed to get the font size to revert a couple of times after a restart, but I can't find a conclusive pattern at the moment.
110% scale, 9pt font size appears to get me back to where I was (or at least thought I was...)
I have a nasty suspicion that something doesn't like altering both the font size and scaling factor at the same time. I also suspect that something is getting corrupted somewhere?
-Leezer-