Two thoughts come to mind:

1) In your patch for the drum machine, using Guitar as Input for Tone 1 and Aux as Input for Tone 2, the best you can do is make sure that you remove all amp and FX processing from both Tones. In other words, use two completely empty Tone setups and simply use the Tone Channel Volumes as necessary to get enough gain to Cubase.

2) Again with the above patch, try engaging the X3 Tuner before you start recording, and set the Tuner to BYPASS rather than MUTE. I think this is the closest the X3 can come to a true bypass.

As you are probably aware because you did not mention it, you can't use the X3L CD/MP3 input for your drum machine for this purpose because this input signal is not passed through the X3L USB connection to your computer.

Hope you get things to work out OK.