Okay, I'll try to explain it the best I can.
Your Apogee Duet doesn't support DSD, it supports PCM up to 24-bit/192kHz. Because of that, all DSD content (including SACD ISOs) need to be converted to PCM to play them back on the Duet but there's a couple things to consider and keep in mind here;
1) DSD to PCM is a lossy conversion, as is PCM to DSD. Both are digital audio formats, but they're different from each other. So any conversion involving DSD goes through PCM and there's data loss involved. This is unavoidable unfortunately, other than obtaining a DSD-capable DAC so no conversion is necessary.
2) Pops and clicks at the beginning of playback
can and
do happen with many DACs and with some are considered normal, depending on the DAC. This can happen when a DAC changes sample rates (going from 44.1 kHz to 192 kHz). You may be thinking that's it's not switching sample rates here but that's not true. First, it's converting DSD to PCM at the highest sample rate your DAC can handle, which is 192 kHz. Second, it's switching sample rates from whatever the sample rate your system uses by default (which you can check and verify via the Audio MIDI Setup app in macOS) to the max sample rate to playback the DSD to PCM converted file. You can also look at Media Center's audio path (furthest right icon of the three to the right of the seekbar) to verify this. Like for example if you have your macOS default output in the Audio MIDI Setup app set to 2 channel 24-bit 48 kHz that means at idle it'll switch the sample rate (to the highest one available) to playback the converted DSD to PCM content. One thing you could try is setting the Audio MIDI Setup app (and thus your macOS system default) to the max sample rate of your Duet, which is 192kHz, and see if that helps any. The only other potential workaround for this is obtaining a DSD-capable DAC
but even then there's no guarantee that'll make the pops and clicks go away, as DACs when switching from PCM to DSD will also pop/click, including mine.
3) Also if you're converting stereo content to multichannel or vice versa, this too
can also cause the DAC to pop/click at the beginning, again, depending on the DAC and setup.
4) If pops, clicks and/or playback stops
during playback of DSD to PCM content (and not at the beginning), this usually means the hardware isn't powerful enough to handle the DSD to PCM conversion. Media Center converts DSD to PCM on-the-fly, which requires a decently powerful enough PC/Mac to handle it. DSD to PCM conversions, especially multichannel conversions, are some of the most resource intensive tasks Media Center can do, requiring fast enough hardware to handle it. Depending on the Mac and how old it is, you may run into this issue. The only ways around this issue are a) obtaining and using a DSD-capable DAC and avoiding the conversion by DSD bitstreaming or b) pre-convert the music of your SACD ISOs to a format like FLAC, Apple Lossless, APE, etc. and play only the pre-converted files back (and not the SACD ISO itself). Of course, this is a lossy conversion (as mentioned before) but you'll avoid the on-the-fly conversion. And of course, this may not avoid the pops/clicks either, so it's something that'd need tested with your setup.
5) Operating system doesn't matter. It'll happen on Windows, macOS and Linux. And the pops/clicks may not happen all the time either, it can be random. Like if I set Media Center to convert DSD to PCM (instead of bitstreaming it) and I playback the Pink Floyd Dark Side of the Moon DSF files I have, it'll pop/click at the beginning of playback on the first track, but when letting it play without manually switching tracks it doesn't pop/click when the first track segues into the second track and it's perfectly seamless without any pop/click. But if I manually change tracks to another one, it'll pop/click then. In comparison when DSD bitstreaming it'll pop/click at the beginning of DSD playback (when it switches from PCM to DSD) but unlike when doing the DSD to PCM conversion it doesn't pop/click when manually switching tracks as long as the tracks I'm manually switching to are DSD and not PCM content.
Ultimately, if the pops and clicks, like I suspect, are caused by your DAC switching sample rates, it's not a Media Center issue. In fact all the points above are not Media Center issues at all, so there isn't really anything for JRiver to look at. The easiest way to avoid pops/clicks from DSD to PCM conversions is either avoiding the playback of SACD ISOs completely and finding and playing back only PCM content or getting a DAC that supports DSD so you can enable DSD bitstreaming but even then like I said there's no guarantees as even with my Topping DAC switching from PCM to bitstreamed DSD also results in a pop/click when it's switching modes (just when switching from PCM to DSD, not when manually switching tracks as long as I don't switch back to PCM).
I really hope this helps.