What is the current state of keybindings (Tools|Options|Keyboard)? What does Tools|Options|ViEmu->Keyboard show?
In any case, I recommend the following process to get everything in VS.NET 2003 to the state you want. I'm assuming you want the Visual C++ 6 scheme, which includes F7 for "Build" and F5 for "Debug":
(1) Remove everything done by ViEmu automatically to date:
(1.1) Go to Tools|Options|ViEmu->Keyboard
(1.2) Click "Restore" under the left list (say yes to the MsgBox)
(1.3) Click "Forget" under the left list (say yes to the MsgBox)
(1.4) Go to Tools|Options|Keyboard
(1.5) Make sure that the current scheme is "ViEmu" (if not, select it from the combo box)
(1.6) Click "Delete" to delete the scheme
(1.7) Select "Visual C++" from the list
(1.8) Click 'Ok'
Now, everything should be clean again. Let's make ViEmu rescan the keyboard and remove & save the clashing keybindings (this shouldn't remove the F5 and F7 bindings):
(2.1) Go to Tools|Options|ViEmu->Keyboard
(2.2) Make sure the list of keys to scan for clashes is to your taste:
"Default" doesn't remove Ctrl-V/Ctrl-C for Copy/Paste, "All" removes those too - click on the desired button
(2.3) Click on "Save and remove"
Now, the left list should be populated with the removed bindings, and the right list should be empty. Everything should be fine.
I also suggest that you download 2.0.33, available from another post in the forum (or from the main download link). You need to manually uninstall ViEmu 2.0.23 before installing this one (doesn't matter whether before or after following the above procedure), but it has many bugfixes and improvements.
Let me know if something doesn't work as expected.