When I asked about what "base keyboard" you are using, I was asking about which based VS keyboard layout you are using. If you go to Tools|Options|ViEmu -> Keyboard, you will see a field at the bottom left called "Current keyboard scheme", which will show it (it's actually a .vsk filename).
Doing Tools|Import and Export Settings|Reset all settings, and choosing a different base keyboard scheme could help with the issue. My VS2008 installation shows five options: "General Development", "Visual Basic", "Visual C#", "Visual C++" and "Web Development". With C++ selected, I haven't found the problem you describe above.
If you just want to get rid of the notification on start up, you can also uncheck the "Scan for clashing keybindings on startup" checkbox at the ViEmu keyboard settings dialog.
- Jon