I can't duplicate your setup, but for me the key was muting anything that could wind up sending the MIDI clock (REALTIME) signal back to the clock source.
You migh start by MUTING every cable port under REALTIME, then just UNMUTE one port at a time to figure out which ones you really need, and which ones could be causing feedback / clock doubling. Remember that you have cable INPUT and OUTPUT ports to contend with.
Keep in mind that if you're using the MOTU USB connection, you'll have I/O ports for all the MOTU cable connections AND a special MOTU "sync" port that shows up under your DAW (working from memory right now since I'm at work, so can't remember the exact name for the port).
I believe the "sync" port needs to be enabled to transfer MIDI clock from your DAW, while the cable connection port(s) need to be enabled to transfer the controller (note, mod wheel, etc.) commands to your synth.
Recommend that once you find a MOTU configuration that works for you, save it as a user preset, then back up the entire configuration file (using Clockworks) to wherever you back up your documents, projects, etc. ~
it would really suck to spend a lot of time tweaking a MOTU routing, then have it dump & have to recreate from scratch!!!
Randy
PS -
I haven't tinkered with this yet with my Minitaur, so I don't know if it is a factor or not~
The Little and Slim Phatty seem to have some "issues" dealing with clock sources other than MIDI clock.
MTC (MIDI tIme code) is definitely a culprit per Amos, but my experience with my Akai MPK seems to indicate that MMC (MIDI machine control) can be problematic, as well. Once I changed to using only MIDI clock on my MPK, and doing another factory reset on my SP, a LOT of seemingly unrelated issues seemed to go away.
In addition to the MOTU routing issues, it might be worth changing your DAW so it sends only MIDI clock as the sync source, and see if that has any impact on the LFO sync issues. I plan to experiment with that myself when I get some free "tinker time"...