When opening version 9.3.1 or earlier MXDs in ArcGIS Desktop 10 that had VBA code in them, the "VBA Detected" warning appears, even after all VBA code has been deleted from the MXD.
If Tools > Options > Require Variable Declarations was checked on in the VBA Editor, but no code was in the MXD, the "VBA Detected" warning is also returned.
This is a known issue with ArcGIS Desktop 10.
The "VBA Detected" warning will pop-up once when performing the 'Save-As', but will not appear when re-opening the MXD.
If there is a need to know what other MXDs had VBA in them, do not select the 'Never show this warning again' option.