I'm going to have to guess that it is.
What I'll do is upgrade to 3.2 and see if it continues. And if it does I'll convert it from 24/96 to 16/44. No matter though, I have the same remastered album but in CD ripped into FLAC at 16/44.
edit: I converted the 24/96 FLAC into a WAV and according to the iRiver its playing at 4608 kBit. I'm going to assume though its still downsampling to the output of 16/44. However, the pops, clicks and glitches have now dissapeared.
Now, I'm a bit of a n00b when it comes to all this but would that be a Rockbox issue since the FLAC had issues and the WAV doesn't, regardless of output bit/sampling rate?
I am using Rockbox 3.1, my next step will be to upgrade to the latest version.