UPDATE: After entering Monolith - Upper Halls, gold is now dropping again from boxes. During this time I replaced Bulwark's Generative Star with Boundless Cornucopia and added 1 passive: Scholar: Purifier's Will

I noticed the same issue with gold not dropping and I am using Scholar\Cabalist\Plaguebringer gates. I have been running with Livor Mortis almost the whole time and gold has dropped. I noticed it stop about Act 3 Republican Backline area. I would only get gold drops off of the yellow enemies or treasure chests, but not from boxes or regular enemies. At first I thought it may have been a connection issue so I logged to main menu, switched to Offline mode and then back to Online, but still the same issue.

The only passives I remember picking up during this time are the following:
Cabalist: Artefact Analysis
Cabalist: Immortal Offering
Plaguebringer: Muscle Stripped Raw (the one closest to Toxic Emanations)
Plaguebringer: Sacrifice of Flesh
Scholar: Steadfast
Scholar: Chemically Empowered Brain

Skills I have configured are:
Anomaly: Event Horizon, Echoes of Infinity, Rending Of Matter - this modifier being the only one on this skill that I changed since I noticed the issue
Aether Jump: Quantum Mind, Veil of Illusion, March of the Time Devourers
Bulwark of Dawn: Haven of Men, Generative Star, Inspiration, Divine Omnipresence - I have changed these skills around several times during this stint of play.
Consuming Embers: Arsonist's Daydream, Engulfing Desires, Heartpiercer, Exposing Flames - this being the only modifier to this skill that I have added recently.
Liver Mortis: Hateful Swords, The Gulf Before Us, Rot's Endless Stream, Hunger Pangs - I added this one recently.

Hopefully this info helps.