Sounds like you have a mismatch in sample rates between audio clips in the same project........ did you record the first part in one sample rate and switch to another (inadvertently) for the bass?
Your card may have switched for you without you knowing, depending on whether you played something on your system in a different rate in between recordings.
Outside of recording s/w, many soundcards self-adjust to whatever WAV you play through them. If your recording s/w was running in the background and you played a clip at a different sample rate, the s/w may automatically pickup on the change, which will affect the sample rates of your recordings after that.
So your project is set at say 48KHz, you recorded your first clip at 48 - then you went back to the OS and played a 44.1Khz clip in Windows or something - the sample rate at your soundcard got changed to 44.1. Then you go back to Cubase and record your bass part - except now, the sample rate in the system has been changed to 44.1, so when you record, it gets recorded at the different rate.
You inadevrtently end up with one clip at one sample rate and another clip at another, which causes one of them to sound out of sync with the project.
I'm not saying this is definitely what happened - only that it's a possiblity because I've seen Cubase do some inadvertent rate switching depending on the h/w involved. To prevent it, I set-up presets in my soundcard settings that lock the sample rate at different rates, so I simply choose the right config for my session before I start and the sample rate stays in place.
