So much of the issue with pops and ticks is system dependent. It can vary with hardware and software. Even a tiny setting change that may not have seemed so obvious at first may be the answer. I am using the latest Jriver on Windows 7, and different configs yield notable variations in the results.
An interesting observation for me is that when using headphones, the tick or click when changing rates or formats is of so little amplitude it is virtually non-existent. I just added a pair of B&W 686 s2 bookshelf speakers to my desktop setup (total impulse buy) and the pops and clicks in this case are more notable. I can think of no reason why this should be the case, other than the gain added in my outboard amp. But as I listen at similar levels whether I use headphones or speakers, it seems that the ratio should scale equally. I am not any kind of expert in amplifiers, though. Perhaps this is due to a serious non-linearity? After all, it is at this point an el-cheapo Behringer amp.
All of that said, I know iFi uses a muting circuit to prevent these kind of things. Also, I believe the latest firmware from a couple months ago went a long way towards fixing these popping issues on the hardware side. iFi is very proactive about these things, but since ( I believe ) the issue with DSD file changes is indeed rooted in the bitstream itself, and will vary depending on the particular software you use, iFi can only do so much on the hardware end, while keeping DSD in its native bitstream.