I have had this issue in the past and resorted to a workaround but am now coming back to using the MC6 as the main driver to managing navigation and activation of presets for MIDI pedals on my board.
At present I have two Empress devices (Echosystem, Reverb), Eventide H9 and a Hologram Dream Sequence. I was originally trying to use the MC6 to control the Empress/Eventide devices and was getting strange behaviour especially with the Empress stuff as this was going through a DA Midibox. I was trying to do PC scrolling and toggling active on all devices but it would only work sporadically and in some cases not at all. I fell back to using a DMC-3xl Gen 3 which had no issues.
I redid my board the other night and had another crack at setting up the MC6. This time round I used the DMC as a sudo midibox using its multijack outs to control the Empress devices.
So I setup 3 sets of 2 presets for navigating the presets using PC Scroll messages. This worked fine for the Empress devices, but the H9 wouldn't work. I then tried with the Dream Sequence and got a similar issue. Each pedal would receive the first PC message and change, but any subsequent messages were ignored. I have been dumping the MIDI out in console to monitor for corruption/validation etc and all looks fine. I spent a long time on this and eventually found that if I sent the bank select MSB message (CC0) before the PC message, both the H9 and Dream Sequence would begin to navigate correctly. But the activate on the Dream Sequence would again only work once and only ever work again if I navigated to the next/previous preset.
So I went back to the DMC and started looking whether this device was sending MSB/LSB for bank select and the only difference I could see between the messages was that the DMC would send the PC first and then the CC to either activate/deactivate (depending on the current state). When toggling the preset however it was simply sending the appropriate CC message with on/off value, which is exactly what the MC6 is doing.
So I can replicate this functionality with the H9 but I can't toggle the active status, i.e. send the PC message, then send the CC activate message (e.g. 42:0/127). I worked around the toggling active by using the H9 toggle CC command instead and this seems to work but the PC scroll has to always activate or always deactivate on each preset.
With the Dream Sequence however I found a really strange behaviour, I can get the device to navigate the presets using either the MSB bank select + PC message or PC message + activate CC message. I can also get the activate to work by sending the CC:23:0/127 + any CC message on a different channel and it works...
MSG1: CC Toggle - 23:127 - 23:0 Ch4
MSG2: CC Msg - 41:127 - 0:0 Ch1
Sorry for the long winded explaination but any ideas why this isn't working?
My only guess is that the H9 and Dream Sequence are expecting more information (MSB/LSB) and left in a waiting state and ignore irrelevant messages. Sending CC messages might be resetting this state possibly????
As for the Empress devices, because the DMC is doing the MIDI to CV conversion it could be making up for the missing messages through its system.