I'd start by viewing the history on ft7800.py in the repo.
Note that the same problem exists with both the current daily and 0.4.0 from over a year ago. (Surely another FT-8900 owner would've reported a regression by now were it a universal problem! Are there any 8900 owners reading this that can confirm that CHIRP works okay with their rig?)
The repo shows 3 changes (Mar 3/4/5 2015) including the one that created the "drivers" directory and moved all the radio files there out of the main dir. The next change ("Fix style issues" -- mostly adding spaces) doesn't appear to have done anything nasty to the code. The most recent change ("Use logging in drivers") just changed 3 instances of "print" to "LOG.info".
I dropped back to the main chirp in the repo's web interface, but didn't see a way to show any entries before March 3rd. (It showed a page of entries, with no "older" or similar button.) The most recent tag was the 0.4.0 release, which took me back another year to March 2014, so I don't know how to view changes between 3/2014-3/2015. Please forgive my ignorance there.