For MCP to run happily with VisualPrefs you need to disable the following options of MCP:
- FrameIHack
- SysIHack
- PropHack
- CycleToMenu
- NewGadTools
VisualPrefs replaces all these features with better ones anyway.
Note that if you want to use MCP's WBGauge option then NewGadTools needs to be enabled, but all of the individual patches within it's edit dialog still need to be disabled.