I have tried updating to the latest mysql workbench version, but to no avail.
Also, purging the current installation and installing from scratch did nothing.
However, today I checked for the error, and my advice to those using linux or ubunut is to check the error logs or the screen output for program crashes.
Well the error here says that
~/.mysql/workbench/wb_options.xml:1: parser error : Document is empty
where ~/ = /home/username
To overcome that problem I simply used the same file from windows installation of mysql workbench (the same version), and it worked like a charm.
in Windows 7, the file is found under C:UsersusernameAppDataRoamingMysqlworkbenchwb_options.xml
if anyone need this file, email me @ email@example.com, and I will send it.