If you're getting noise, that typically can be traced to a MIDI cable that isn't shielded properly, or in some cases, can be traced to a ground issue. In the rarest cases, some MIDI enabled pedals have some bleed between the MIDI signal and audio. Going through your rig and figuring out where the noise is coming from and/or measuring your cables to see if they're properly wired are good ideas.
MIDI clock is supposed to be continuous, per the MIDI spec. The intent for this is to keep multiple devices in sync with each other at all times, so they can't drift apart.
That said, the continuous clock requirement makes more sense in the synth and sequencer world than it does in the guitar effect world. And, clock synchronization issues were more prevalent in the old MIDI days when computer hardware wasn't as good as it is now. As of firmware version 5.2, there's a "Clock Pulse Limit" parameter in MIDI Settings that lets you set a limit to how long the clock runs each time the tempo changes. Set that to 10 to try it. You may have to add more if your pedals aren't syncing up, or you might even be able to reduce the number, depending on your hardware.
