Hi Will
Since that is saved individually with the file I have a couple ideas that seem very simple but may help.
First are you saving the file? If I open a file, change the "Quad Tree Mesh Parameter" then close THERM without clicking save when I open the file again then I see the Quad Tree Mesh Parameter value has not been saved. But if I then change the Quad Tree Mesh Parameter and save the file when I open it again the value has been saved. So maybe explicitly saving the file after changing it might help? If it gives you any error messages when doing so please let us know.
Second are the files somewhere you don't have write access to? That could potentially be preventing the changes from being saved as well.
If neither of those work what version of THERM are you running? You can find that in Help->About. Please give the first three sets of numbers like 7.8.80 or 8.1.30. No need for the dll versions.
And if possible could you send a file you are having this problem with? If you don't wish to post it publicly you can contact me directly and we can figure out a way for you to send it that way.
Thanks
Stephen