I know exactly what you mean and I do see your point. I think the problem might be due to the daisy chaining rather than the nature of MIDI clock data itself. The bypass looping equipment is currently after the Eventides for this very reason, but it might make sense to try out one of those MIDI Solutions MIDI THRU boxes before I give up and resign my entire live rig.
I do understand that these stompbox units were intended to fill an existing void in the ever exploding high end guitar effects pedal world, but with the exception of the Pitchfactor, the Eventide pedals don't exactly make up the bread and butter of my sounds. That being said, the Timefactor and Modfactor sound fantastic and do almost everything that I need them to do to add some flavoring at the end of my chain. I gig a lot and feel like these pedals have definitely helped me break into the live hip hop and electronica scene as a bassist in a really great way. I bought them because I didn't want to rely on a rig any larger than a head, compressor, cab, and PT-Pro to do what I have to do.
So, I'd definitely be interested in any workaround ideas. I'm really satisfied with everything on my board and if I can resolve this issue, I'll be done with gear for a really long time.