You cannot switch BDB versions on a wallet that wasn't cleanly shut down on the prior version, I'd guess thats whats happening here.
As I understood it is a brand new instalation where the wallet.dat isn't even present yet and had to be created.
running bitcoind_broken or non-stripped bitcoind executable as root OR user bitcoin (su - bitcoin -> ./bitcoind) make no difference.
Edit:
.bitcoin is NOT created if i run as root
.bitcoin IS created if i run as "bitcoin"
.bitcoin is probably being created on /root/.bitcoin when you run it as root (unless you define datadir on the command line)
Anyway, if it was created when you run it as bitcoin user then it is not permission problem indeed.
drwxr-xr-x 4 bitcoin bitcoin 4096 Nov 30 22:47 .
drwxr-xr-x 3 bitcoin bitcoin 4096 Nov 30 22:47 ..
drwx------ 2 bitcoin bitcoin 4096 Nov 30 22:47 database
drwx------ 2 bitcoin bitcoin 4096 Nov 30 22:47 database.1385848052.bak
-rw------- 1 bitcoin bitcoin 102 Nov 30 22:47 db.log
-rw------- 1 bitcoin bitcoin 1264 Nov 30 22:47 debug.log
-rw------- 1 bitcoin bitcoin 0 Nov 30 22:47 .lock
-rw------- 1 bitcoin bitcoin 1106 Nov 30 22:47 peers.dat
If you remove the /home/bitcoind/.bitcoin/ and start bitcoind again, does it create again the same files as stated above?
Adriano