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The guitar port is working fine
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How do you know this?
I'm assuming your guitar works fine on other amps and such so the problem is somewhere between the guitar cable and the ouput of Cubase.
It could be your guitar input / soundcard thingy. (Which you don't think it is).
It could be how you have your input set in Cubase. Press F4 and see if your inputs are selected to your proper soundcard.
Does your soundcard thingy have a mic input? If so, I'd check to see if you can get anything into Cubase with a mic. If you have a second channel, try that too.
I'd check the control panels to make sure that your audio interface is still the default sound card.
Let me know if that gets you anywhere.
Brandon