Had a not so smooth update. Anyhow I've manage to get everything working back again. Some plugins really gave me some problems (daap and website, had to edit manually the dpkg status file there). Had several problems with the dist-upgrade and apache2, I think it was because some customs virtual host (bt.lan, coach.lan, cups.lan, etc).
Had to build again my deluge daemon. I was surprised that my custom build of rar2fs survived, so no problems with Plex there (I havent test PlexConnect from the atv2).
Boot parameters for the kernel survived through the update. The grub-update had some problems with my 40_custom entry for my gparted, some syntax error, had to delete it coz it wasn't booting on kernel 3.2 and then grub produced the new entries with no problem. I'll take a look later what went wrong there. FTP access and Rsync backups working. So far so good.
Anyhow I was looking at the service section in samba and I saw some warnings, I don't if is worth looking into the settings of the SMB section of OMV
WARNING: The "printer admin" option is deprecated
lp_load_ex: refreshing parameters
Initialising global parameters
rlimit_max: increasing rlimit_max (1024) to minimum Windows limit (16384)
params.c:pm_process() - Processing configuration file "/etc/samba/smb.conf"
Processing section "[global]"
WARNING: The "null passwords" option is deprecated
Processing section "[ricardo]"
Processing section "[global]"
WARNING: The "printer admin" option is deprecated
Processing section "[printers]"
Processing section "[print$]"The shares still work, i can access them through my vpn at work.
Anyway thanks for all the effort put in this software 
, now is time to read ngnix manual for fixing doing the virtual host entries.
greetings
Update:
1)For flexget I had to "pip install flexget --upgrade" to update all the python dependencies.
2)Another thing after the update, Cron keep sending me this message to my mail:
PHP Warning: PHP Startup: Unable to load dynamic library '/usr/lib/php5/20100525/suhosin.so' - /usr/lib/php5/20100525/suhosin.so: cannot open shared object file: No such file or directory in Unknown on line 0
An apt-get purge php5-suhosin fix it.
3) My custom monit for deluge and transmission no longer work. I think the custom monits are located in some other place now.