I also just upgraded my DAC to the latest SEG from Stan just before Christmas, I have a Denon DCD 520 which I use via the optical out into the DAC, to be honest I've not heard and pops ? I have my Pioneer Network Player connected to optical in, so I can swap between 1/2 and I did a test playing the same track on the CDP and FLAC from the Pioneer, I didn't notice a pop even switching while the track was playing on both.
Update
In the TV break I switched the Denon CDP on and connected to the SEG =No Pop volume on my amp was at the 9 o'clock position and loud enough any pop would frighten you. I tried it also just off 0 volume.
Playing a track, pressed the power button off =No Pop
Switched the Denon CDP back on =No Pop
Switched between the Pioneer Network Player and the Denon CDP =No Pop
No matter what combination of Power On/Of I can't reproduce the pop your hearing. Maybe its Marantz CDP and their output to the optical out is causing the problem?
Do you have any mates you could borrow another make of CDP off and do the same test?
Amp Rega Elex-R
CDP Denon DCD 520
Tuner Teac T-R650 Dab/FM
Music Player Pioneer N30 Network Player
DAC Rega Dac-R
Speakers Q Acoustic Concept 40s
Speaker Cable Current is Rega FSC Quattro , Fisual S-Flex Studio 2.5mm / Ortofon SPK 100
Interconnects Van Damme Silver Plated OFC Pro Classic XKE CDP/Tuner & Solid Silver Cyro 99.99% Pure, Dac To Amp
Headphones AKG K550 mk3
SUB BK XLS 200