Are both LFOs for each tone sync'ed to the sequencer ("Ext Sync=CLK")? Is there any delay time set for the LFOs?

Altering the LFO wave shapes will change how "tight" the LFO-controlled sound is when sync'ed with the rest of a tune. Also, the type of waveform of the sound itself will also impact this.

Remember, if you modify a user patch which you're using in a sequence, you have to rewrite it to user memory, then reselect it in your performance for you to hear, in your song/sequence, the changes you made.