[Sardi]

I'm pretty sure that Vacum's LFO doesn't sync to tempo hence why your wobbling is going out of time.

Best bet is to either do it in a different synth, or automate the filter cutoff as mentioned above. Make sure you un-assign the LFO to control filter cutoff, then draw in filter automation in your MIDI editor.

The good thing about doing it this way is that you can draw the automation in different timing intervals which is the way most Dubstep wobble bass works anyway. Even if you did have the LFO sync, you would more than likely automate the LFO to achieve the desired sound.