If it is what i think it is there may be solution .
I'll try to keep it short - there 're two ways midi can enter Skewbase SX - either via "Direct Music" midi or via "windows midi" (its turned on/off in device setup/midi )
These are two "different" ways of how cubase interprets midi events transmitted by your midi interface .Depending of your version of cubase it's either "direct music" or "windows midi" turned on by default
You may notice that windows midi page is blank (nothing listed there ) if direct music is enabled and vice versa - why ?
Because some programming genious in steinbug headquarters tought it's actually intelligent and cute to hide these choices and it's default changes from version to version ???
Doh
Anyway to try to keep it short again - there's a folder inside main Cubase folder called MIDI Port Enabler with file named "ignoreportfilter" with no extension and its size is 0 bytes OR if you're using 3.1 version and above there's file called enableemulated also with no extension and 0 bytes in size .
All is okay -close cubase then copy that file to main Cubase folder (where Cubasesx3.exe is ).
Now you should see your midi interface listed in both direct music and windows midi pages and you can set what you want to use in "show" column on the right.
If you set Direct music to show on - turn it off in windows midi - simple.
Now it's time to test timing to see is your selection okay - turn on audio metronome and record 8th notes like madman right on click -pling,pling,pling few midi channels few bars .WHen you play it back it should sound okay as you played it .If it's not change your windows midi or direct music choice and you MUST restart cubase after every change .Ugh i forgot there's one more option under DIrect music called "use system timestamp" - thats actually "third" method - one of them will work - it's different for every midi interface - "older" midi interfaces mostly work with windows midi and newer with direct music with system timestamp turned on .
Jesus i can't beleive i'm actually quite calm while typing , i remember i wanted to send antrax letter to steinberg during discovery of all this crap
Note - there's a posibility that you still cant see both pages listed cause of that stupid filter thing - you can make that "ignoreportfilter" 0 bytes file yourself if you dont have it ,just make new text document name it "ignoreportfilter" and delete its extension .
ANyway good luck with it post some detalis if you don't solve it we'll nail it