Did you follow these instructions before you installed MP6, if you did you should not have any problems! MP6 requires this upgrade before you install it.
FPS Creator Upgrade 1.04
The subtle number increase from 1.03 to 1.04 belies the massive number of changes that have gone on under the hood in this revision. There are no less than 58 changes including new features, enhancements and fixes. Multiple public releases of the upgrade, and beta tester feedback as we went, has all contributed to the best version of FPS Creator ever.
To ensure a smooth upgrade process, follow these guidelines:
Uninstall any update you may be running on your system (1.02, 1.03, 1.04 betas)
Download and install the new 1.04 update
Note: If you have model packs 3 and / or 5, we also advise you uninstall these are re-download new versions of them from your Order History. The original packs included FPS system files inside them and these are now old and redundant. You can identify the new versions of the Model Packs because when you download them they'll have _07 on the filename, for example: FPSCreatorModelPack2_07.zip