I just tried this out as a simple test and it seems to be a problem if you enter the meter first and then try to change the barline. It works, though, if you have the repetition barline there and add the meter change later. So it can be fixed by deleting the local meter (the repitition shows up where it should) and then just reentering it at the same place (opt+Enter).
Of course it should work the other way around, too, so I consider this a bug/unexpected behaviour… let me know if this works for you!
PS: Derrek’s Workaround seems to work, too, you may reenter the repetition barline before the custom meter change via popover: Shift-B, type in “end”, alt/opt+Enter; or just alt/opt+click the repeat ending in.
PPS: Both workarounds seem to destroy playback, resulting in an endless cycle of the repeated part, suppress playback for the local repetition ending does not seem to help. You can turn off to play repetitions globally in the playback options, though, to get to the end of the piece.