One thing which can make your custom MIDI file NOT load, is if it contains a parameter which is "invalid". "I swear that I loaded the file!" - yes, I did, but it contained an error - it won't load until the error is cleared.
Got me caught a few times. Just scroll down the interface looking for that word and change value to something recognised. Not saying it's def the problem you're having but it could be.
There's is of course more..
Posted recently about how to save your MIDI setups in Pianoteq.
You can save your MIDI custom files as "G" (of course, global by default), or by clicking on the G, you then see "P" (just per preset).
Look for the little G icon in the left side of the interface (eg. lines beginning with 'controller' 'pitch bend') when saving out your custom MIDI file.
If you save a custom MIDI file by clicking the G so it becomes P, then it will load automatically any time you switch over to that preset.
There's some detail in that above link.
To solve A/B testing issues, I always right-click the save icon and 'save as' a new preset. This allows me latitude for loading custom MIDI (IF I want to A/B that - otherwise, it doesn't matter 99.999%). If working A/B on exact same preset, it will only allow the custom MIDI you saved to work (if you set custom MIDI, save "P" style, use as A, then also use same preset for B, then when you edit B's MIDI but don't save it to preset, of course the A's saved MIDI will load when A/B between the two. Again, solved by saving "P" style only (forget global defaults unless you know you want that).. then you save a clone to work on as your B
So, best thing to do IMO to cover all bases, is save "P" per preset.
Sure make a global sane one by all means if it's useful, and/or just keep using the existing global one for startup (probably what most will benefit from). On all pianos you use and want your MIDI file, just load your MIDI file and save the preset while it's loaded in
Pianoteq will just go ahead and load the default - then make additions/subtractions in MIDI which exist now for your preset. Great if you want your Harp set up like a piano (pedals etc).. you never have to again flop around looking for files to load. Make your change (pedal up instead of down etc) and it's attached to the preset. If there's another preset you want to attach those changes to, come to that bridge and cross it by loading your file and saving that preset.
It's more work - but if you only need one global file, go that way. Caveat, if you're altering MIDI setups for different environments, chances are trying to have a selection of different global files might end up just as, or more work.
I've tested around all the above etc.. but if I'm mistaken - always love to learn - feel free to let me know.
Pianoteq Studio Bundle (Pro plus all instruments) - Kawai MP11 digital piano - Yamaha HS8 monitors