I don't think the R-D1's especially flakey - it's components are the same quality as, or better than, the Voigtlander Bessa R3/R4 cameras, and in many instances the parts are probably identical (or near enough), yet the Bessas haven't gained a rep for especially poor rangefinders are jamming shutters. Like others, I've had to adjust my rangefinder twice (once after I dropped the camera), but after adjustment it stays calibrated, and my camera's otherwise been totally reliable. Anyway, sooner or later any rangefinder will need its focusing checked and recalibrated.
I think one reason for the R-D1's poor rep is the fact that it's digital, and being able to see huge images highlights any problems - I suspect that if photos from a random selection of film rangefinders (all makes) were enlarged similarly, their owners of many of them would be horrified at how badly their cameras need servicing!
Anyway, turning to the viewfinder. The angle at which the focus patch is viewed does seem to be critical - I try an keep my eye perpendicular to it. Also, I find all cameras (not just the R-D1) extremely frustrating to use with glasses, and wear contacts if I know I'm going to be taking photos. With glasses, I often can't see everything in a viewfinder at once: if I can see the focus patch, then I can't see the shutter speed; if I can see the framelines, then I can't see the focus patch... Drives me bonkers!