Are you using the 32 bit version of Windows Vista or the 64 bit version?

You can try this:

1. Close Cubase
2. Open the Program Files folder on your C drive.
3. Open the Steinberg Folder
4. Open the Cubase folder
5. Open the MIDI Port Enabler folder
6. Right click on the ignoreportfilter file and select CUT.
7. Hit the Back button in the window.
8. Right click inside the Cubase folder and select PASTE.

When you follow these instructions, you are cutting and pasting the ignoreportfilter file from the MIDI Port Enabler folder to the Cubase folder.

9. Then open Cubase

You will notice 2 listings for the same MIDI input in the MIDI input routing dropdown menu in the Inspector column. One will have (emulated) next to it. Select the proper MIDI input that has (emulated) next to it and record using that port and see if you still have any MIDI data shifting when recording.

Hope this helps.