However, although the tempos are showing the same, the flashing tempo LEDs are not synced. This was true in both cases: one H9 synced to the other and both synched to the Tempode clock generator. This is a little troubling. The tempos read identically in BPM but the LEDs are off by a fare margin (almost 180 degrees).
MIDI Clock doesn't have a concept of beat or measure position. It's just sending out 24 ticks per beat. The way to synchronize the tempo to a particular beat position is with MIDI Start messages, and the H9 algorithms that are sensitive to beat position like the HarPeggiator and Looper listen for MIDI Start messages. For a lot of the algorithms the actual beat position doesn't matter though. For example when you're using a delay algorithm, the MIDI Clock sets the tempo which affects the delay times; if you play something on the first beat, then it's delays are going to be in time with the subsequent beats. So, in that case the H9 doesn't need to know when a measure or beat is beginning; if you play at the correct time, the delays will occur at the correct time.