I applied the 3.0 Upgrade but I see a different version number in the Main Menu

The CMBN v3.0 and CMFI v3.0 Upgrade show an internal Build number in the menu screen (v2.20 for CMBN and v1.20 for CMFI currently). That is correct and indicates that you have the 3.0 Game Engine Upgrade installed correctly.
Published on: 2014-08-11 See other articles in CMx2 (e.g. CMSF, CMBN, CMFI, CMRT, CMBS, CMFB), CMx2 - Upgrades.