Hi Dan,
First, you can thank MBH for me taking the time to look at your files she had "girls night out" tonight and I was bored.
Now for the fun part, I took your files and created my own test project to see what would happen. I too could not get multiple levels on one sheet without getting interference symbols. I then created a view with both levels in it and it looked as I would have expected (ie with the mezzanine in the correct position.)
What I ended up doing was shifting the mezzanine level 100' east in the view drawing and this allowed me to create a multiple level sheet with no interference symbols.
Since I'm not an Architect I'm not sure if this is the solution although I have received many drawings from Architects that had done just that.
If you would like to see my test project PM me with your email address and I will send it to you. The e-transmit file is over 10 mB otherwise I would post it here.
Hope this helps,
BTW: Very nice work