it’s something on my end/chain, which I hope to isolate and share in case others come across it.
This is what I´m hoping as well.
That´s why I´m sharing the knowledge/experience of some manufacturers occasionally deviation in some of their products. It always strikes me with a bit of surprise whenever I come across these units, but that´s definitely just because I´m aware of what the MIDI standard is (being as geeky as I am). Otherwise I probably wouldn´t even have noticed the deviations.
I´ve recently seen a few posts at the FractalAudio forum, where people are asking about stuff that you would easily be able to answer for yourself if you just searched, read and understood the main basics of the MIDI standard. But I realized then that I can´t really expect others to be as geeky as myself with something that was set as far back as in 1983, and which haven´t really been updated since (which some even finds obnoxious in that sense!).
These other people may be a bit younger, or just not that interested. But if they come across one of these units with Soft Thru (and/or merging) first AND at the same time learnt that this thing that´s called MIDI (with the funny connectors/contacts) is apparently an old standard every manufacturer keeps themselves to. They might get a few things slightly wrong because of their units being a bit different. Which could lead to some confusion later…
That´s the main reason of my post, to have others getting the opportunity finding it in a search. Sorry if I/we got you offended in any way, not our intention.
Now, regarding your problem:
Could it be bandwidth overload? (if there´s some other commands being transmitted as well)?
Bad cable?
I just recently had an interesting “fault” with Bank Select messages being sent (first, without me knowing why) from a footcontroller. But when sending new Bank Select messages, nothing happened. Still recalled presets in another bank. It seems that the only solution that did work, were power cycling the receiving unit. No problem since (knock on wood).
But that kind of problem with that kind of solution doesn´t help you if performing live… 
By the way, I am a bit curious of what interfaces and/or brand you´re programmer for (music business?). If you are willing to share that info?