Go to device menu – device setup – and on Windows MIDI or direct music
and check use system timestamp.
If that does not work go to C:\Program Files\Steinberg\Cubase SX 3\MIDI
port enabler and copy the file ignoreportfilter to C:\Program
Files\Steinberg\Cubase SX 3\. You will then have an emulated and non emulated MIDI ports. Try changing them to the other choice, often non-emulated.
This is explained during the installation of the program. You can learn more at http://knowledgebase.steinberg.de/95_1.html