[rt-users] can't get rt to use innodb

[Tom Vier]

I recently upgraded to rt3.4 and noticed that with every comment, a 
blant comment appeared before it. I get this in syslog:

Jun  6 15:55:09 opteron-prime RT: DBD::mysql::db rollback failed: 
Warning:  Some non-transactional changed tables couldn't be rolled back 
at /usr/share/perl5/DBIx/SearchBuilder/Handle.pm line 721.  
(/usr/share/request-tracker3.4/lib/RT.pm:277)

I used to have "skip-innodb" in my.cnf, but i removed it, and restarted 
mysql (debian version 4.0.24-10, btw). It created the log files and 
phpmyadmin indicates that it's running, but rt still has the same 
problem. I even cleared the session cache, but it's still not working.

Am i missing something? tia!