I don't believe seph put out a BBM that supports the new patch yet. Any theme (not just BBM) will lose the transitions if it is installed (unless stated otherwise). The transition is basically a few lines of code built into the theme's framework, what the patch does is modify the framework to enable it, however; when it does that, it over writes the custom theme... its a 2 way street, when you install a theme, it overwrites the transitions.
Short answer, you cant have both, not yet anyways. I'm sure Seph is working on an update for it, same with myself.
For now, pick what you like more, a theme or some fancy window transitions on the stock look. Your choice!
5.2 is up... But it's essentially a copy of 4.1.
Difference in framework-res.apk from 1.8.6 to 1.8.9 to 1.9.0:
1.6.0- First framework-res.apk from the framework also used in 1.8.x/1.9.x
1.8.6- moved text off center (clock, date, verizon wireless (or modified text) on lock screen (for vanilla look and feel)
1.8.9- Added transitions
1.9.0- EXACT framework-res.apk from 1.8.6 (only difference is /res/layout/banner from 1.8.6 was removed... identification file for drod, to help determine if his work had been kang'd...)
I haven't done a file compare on 1.8.9 with the 1.9.0 transition patch.. but if I was a betting man, I'd put odds that it's just 1.8.9 framework-res.
tldr;
So, if you want transitions, grab my 1.8.9 barmod. If you don't, grab my 1.9.0 barmod.