First off, try increasing Sonar's MIDI buffers to at least 500.
If you still see odd behaviour at times, try resetting the audio engine and MIDI (the icons to the left of the tempo in the control panel.
The step sequencer can be glitchy at rare times (misses notes, mistimes notes, and finally resorts to outputting random MIDI notes) and resetting the audio engine and MIDI usually brings it back to its senses. Failing that, try saving the project then re-opening it.
I reported this as a bug about three versions of Sonar ago but it seems to have persisted :-(
Of course, your problem may be something else......
In which case, does it only happen in one project?
As for bass lines, the step sequencer's forte is when you want sequences that sound sequenced. It can work well with synths, but for a more "natural" bass sound I'd suggest using the piano roll. Amongst other things you can record/draw controllers in the PRV much more easily than in the step sequencer.