Already answered my own question.
We use SyncDek for auditing purposes. I realized that a few steps in our startup script, which basically check to see if the required plug-in is installed, has been disabled. This meant that for installs of FM (I'm now assuming Pro or Adv) that were accessing our solution for the first time were not having the plug-in installed, which was nullifying the calculations used by SyncDek in the security settings (because it couldn't find the functions used by SyncDek).
Thankfully, all it required was enabling those script steps in our startup and everything is working fine now.
Clearly, my "newbie" description is accurate.