This should not be the case if you are using a recent version of the plugin and the walls of the rooms between floors are actually touching one another within the tolerance:
Do you want to send a POMF that recreates the issue so that I can tell you what is going wrong for your case here?
I am just making a note here that we determined over PM that this issue was caused by using an old version of the plugin. When using the latest version, all of the adjacencies are correct as long as “Solve Ceiling Adjacencies” is checked.