[dave256]

While it's not impossible that there was a connection between the security update and your permission issues, I would say it's unlikely applying the security update broke OmniFocus for you. I've been running OmniFocus since June and have not had any issues like this. Of course it's always a good idea to have a complete backup (ideally a cloned backup you can boot) before applying operating system updates.

If you have a problem like this in the future, I would ask for help in resolving it (I seem to recall a few other posts about permission issues with OmniFocus that were not related to the security update) before doing something as drastic as an archive and install. I hope this advice helps you in the future.