From the description in the manual, the Run and Tempo parameters seem to conflict. It doesn't come right out and say so, but each seems to want to do different things to the LFO waveform, depend on what's going on at a specific time.
Also from the manual:
Reading between the lines again, it would seem that if you can program your MIDI pedal to send a rapid Off-On command sequence, you may be able to keep the LFO in time with an occassional tap of a footswitch.
That is what the run parameter is supposed to do but instead of using a quick on/off you are having the envelope do the off then on.