This has been happening to me for over a year (we started at trixbox 1.0 and currently use 2.2.4 with freepbx 2.3.0, upgraded today which bit me again so I'm writing it up).
We have 45 extensions. The defaults for FOP are 40 cells for extensions. Each cell grouping when it reaches the end will restarts at the top left cell and over writes the previous ones.
I've found and made changes in the retrieve_op_conf_from_mysql.pl, op_style.cfg, op_buttons.cfg, op_buttons_additional.cfg, and op_server.cfg
files with the proper values for our setup so that our slightly smaller buttons fit now in three columns along with our 26 trunks.
But every time we upgrade the install scripts just go ahead and over write the previous version files without prompting about a existing older version and giving me a option of doing a diff, overwrite, yes, no, etc. so can do something before I loose my pain staking changes we've done.
At the very least for the retrieve_op_conf_from_mysql.pl file can values that define cell postitions be moved into a install non-overwritable config file some place and have it read out from the FOP webroot/panel directory where all other settings are stored?
It would be nice if the install also prompted about overwriting of those files for those of us who make changes to them.