The R-1 internal mikes do record the noises from compact-flash cards... and some cards are noisier than the others. The Kingston 2 Go noise is obvious when recording with high gain, but the Roland 64 Mo card also make noises when writing data (though it's quieter than the Kingston one).
Check this:
Go to a silent room, put both the record level and headphones level at maximum (be careful of the Larsen if you're using open-structure headphones!! don't damage your ears!), no line in or external mikes plugged, and launch a record: you'll hear that the ticking is clearly audible when data is written on the card, but not when the recorder is paused. Using different CF cards produce different noises, but I've never met a perfectly silent one yet.
So... I solved this problem by using external microphones. And I'll soon get a good external preamp, because the internal one is far from fantastic (and I need phantom power).
The R-1 is a nice, convenient, small and very useful device, though! Just bypass its preamp and avoid the internal mikes if you want the cleanest recordings ;-)