The problem with FT not appearing on some items appears to be tied to how it's entered on the item.
Compare these two items. Both have FT3 or Mana Regen 3, depending on which terminology you prefer.
Blessed Coldain Prayer Shawl
https://everquest.allakhazam.com/db/item.html?item=11999 FT is recorded as a Flowing Thought effect.
Signet of the Arcane
https://everquest.allakhazam.com/db/item.html?item=20379 FT is recorded as "Mana Regeneration" under Additional Modifiers.
On my profile, the Shawl is counted for FT, the Signet is not. The entry for the Signet doesn't display the mana regen at all, though the focus effect is shown.
https://everquest.allakhazam.com/profile.html?377692 Assuming that I regen zero mana per tick while standing (without any gear, that is), then the profile is correct -- it counts the three Mana Regen from the Signet as "Base Standing" Mana Regen, and it counts the six other mana regen (from the Shawl and my Jaylia's Boots) as "Worn" Mana Regen.
I think you just need to look at how the profile system handles "Flowing Thought" as an effect and "Mana Regen" as a modifier.
Hope this helps you nail it. =)