Check out the Release Notes – Other Changes for the version 5.4.0 firmware on the ModFactor product page.
LogicPro should be able to send a MIDI Start message to initially sync, or re-sync the Modfactor. Barring that, you might be able to send (any) MIDI CC message (with a value of 127) to the Tap function. Pressing Tap restarts the LFO waveform. Works on the H9, so try it out on the ModFactor.
Another thing to check is the WIDTH control in TremoloPan. At zero, it’s left & right in sync. At 99, left & right alternate, and it ‘feels’ like twice the SPEED. Intermediate settings place the right channel between 0 and 180 out of phase with the left channel. Those values can make it difficult to hear the sync clearly.