I think I have encountered the same problem with the new patch. Playing as Germany, transferring control (send expeditionary force) of an inf corps to another country, say Spanish Nationalists and then bringing them back under my own control again seems to prevent this corps from ever boarding a german transport again.
All the time I've got the two transports (both in a single group)sitting outside Wilhelmshafen.
Before I sent the corps as an expeditionary force I could walk them onto the transports.
After they were put under Span.Nationalist control I could NOT walk them onto the transports (but walking to another province is possible).
Now, after placing them back under my (German) control again, they STILL cannot board the transports. The corps was in the same province all the time and the unit composition did not change.
Smells like a jolly old bug don't ya think?