Haven't had this problem before but might have something to do with the large size of the assembly. All of the cabinets are supposed to have the dado with pocket screws but as you can see some do not. I have tried going to butt joint and then changing back with no results. I can probably turn face frames on and off to rebuild the cabinet but wanted Scott and the guys to look at it first.
Follow up, I ended up having to delete the offending cabinets and starting over. Not a big deal only took about 20 minutes but still would like to know what Scott finds out. It could be a bug or could just be one of those things with big assemblies and lots of part edits where it gets lost or hung up.
It is most likely due to the bld 13 issues with the joinery not switching/switching off that we resolved in bld 14 (you just had it stuck in an odd state so to speak). I will look into it as soon as I can and try to confirm that, but my guess is that you will not run into it again.
Follow up on this. I am having this issue with a bunch of cabinets but did figure out if I go to pocket screw tab and then select apply to cabinet it will apply the slots even if there is no hardware selected. Go figure.