This is most probably because your midi pedal is sending too much data too fast for the H9. Some people are using the Moog MP-201 in a similar way but found out that they have to use the "midi governor" setting on the MP-201 to reduce the data rate sent by the MP-201.
There's a link to a full discussion about using an MP-201, which somehow would apply to using any brand of midi pedal with an Eventide stompbox.
http://forum.moogmusic.com/viewtopic.php?f=10&t=7668&start=0
Note that the last comment says that reducing the midi data rate did solve the problem, which was the same as what you're experiencing.
LA
