I'm seeing the Mayor package as currently selling for $300, not $250. The Magistrate is $550, and the Governor is $800. The prices you quoted have been replaced long ago. I'm guessing you had a version of the Mayor package, that sold for $250 before the price increase last year? I'm not sure why it will allow you to upgrade to your existing package though. The Magistrate should be $300 for you, not $325. Likewise, the Governor should be $550.
On your profile page, click on "Influence" on the left side and make sure it's crediting you with the full $250 spent (ie 2500 IP added for that purchase). If it applied a credit, discount, or anything else, that might play into it. I'm just as confused as Violet about that $25 difference on the two packages vs the Mayor though. Something certainly seems off.