Why am I having trouble finding secrets?

Finding secrets and traps seems to rely entirely on the Mechanics skill, not Perception. My main character has a terrible perception (3) but high mechanics skill (7) and has no problem finding secrets.

As you mentioned, you will need to be in scouting mode and walk near the secret. If you detect it, the secret will turn purple (as in the below screenshot) and your character will mention spotting something hidden.

Waiting around and speeding up/slowing down game time does not seem to have any effect, you either find it immediately or need to come back with a character with better Mechanics skill.