hi ckett, have you tried setting the buffer higher (e.g 256 or 512)? Try it and see if the click goes away. If it does, then that's you're problem - although the RME device will run at extremely small buffer sizes (i.e. low latency), it depends how well your system is optimised.
You should be able to run at 512 buffer size without noticing much latency in operation (it's 12 ms I believe), unless you're monitoring through the DAW itself - if you use the RME mixer for monitoring you can have the buffer size as high as you like, still with near zero latency for monitoring.
Is there any chance that you're using your audio interface as the 'everyday' (default) system audio player, probably at 44.1 kHz, but that you're using a different sample rate for recording?
That might account for the device switching sample rates every time you change modes, with it snapping back and forth from the default 44.1 to your DAW SR (48, 96, whatever)... and that might cause such pops.
It's that sort of thing that has always kept me from simply setting up my 'serious' interface as the system default interface. (I simply use the SB-clone built into my motherboard as the 'everyday' player.)