I’ve had similar problems with synching Harpeggiator (and other H9 pattern/time algorhithms) with MIDI clock. When you change presets with clock running, the presets sound scrambled. You have to stop whatever is sending sync, wait a couple of seconds and restart with the preseet you want selected. This is a real bummer.
A workaround in software: Disable MIDI clock in the H9 and set the H9 to receive tap tempo info on a MIDI CC number (via MIDI Settings>Assign MIDI CC to pedal functions>Tap Tempo). I used CC 50. Then in Ableton Live I made a 1 bar MIDI clip with 4 CC 50 pulses drawn in that sends tap tempo pulses out to the H9. This seems to work flawlessly. The only thing is that some presets to do not start at the beginning of the pattern. But this can be fixed with either a “restart” command or calling up the preset again (via a MIDI button or MIDI command mapped to that preset.)