Sec31Mike said:
In Endgame when she did use a cloaking device, she was future, bitter Janeway. Maybe the Federation could use cloaks then, so maybe it wasn't against the treaty anymore.
Actually it wasn't fully a cloaking device, it was referred to as Stealth Technology.
I have always viewed it as being along the lines of the technology used by the Kazon. The Kazon used Masking Circuitry that minimized their sensor profile to the absolute minimum levels. The ship is still visible (and Janeway's shuttle was still visible while near the Unicomplex) but sensors can't lock in.