With Mint 14, the new Mate-Calc V1.4 doesn't show the thousands separator even when the box is ticked in preferences, I read this wont be fixed until version 1.6, which I assume means it's not seen as important.
The solution right now is the install Gcalctool V6.6 from the repos, the thousands preference box works in this one.
I did also see some talk of this being a "regional" issue, I have my region Australia, I wonder if you have US language and region this problem doesn't exist? This might explain why the devs have seemingly put this on the back burner. I use the calculator daily, and it's a night mare dealing with large numbers and no thousands separator.
Anyway I am glad there is a work-around.