Weird Transposition bug?

So I'm writing a piece for a small ensemble, one player is responsible for both E-flat and B-flat Clarinet parts, and they switch off throughout the piece. I made the part work on one line by hiding empty staves and putting horizontal breaks in places to stop both staves from being visible at once. I write in concert pitch because its faster, but when I swapped back I noticed some passages had been made weird, specifically E-flat clarinet passages with tuplets. For instance, these two passages sound the same, the one with E#-G#-A-C# is concert pitch. Another example happens with this but instead going down an entire octave.
The third screenshot is what the piece sounds, and the 4th is what the part shows, this is also for E-flat.

Also worth noting is that the pitches are incorrectly placed on the staff, but are shown on the inspector to be the correct tone, Ie the written B#4 on the transposing score shows as B#5 on the inspector, and sounds as B#5.

What can I do to solve this? Do I need to just type out a seperate part for these instruments or something? I might be doing something stupid, but given that it only occurs on e-flat parts with dotted rhythms within a tuplet, I suspect it might be a bug?