Make sure the rim-tape is seated in the well of the rim and doesn't get up on to the shoulder at any point. I had this happen to a rim on my Schwinn - it had a Velox rim-tape which was sticky on one side and over a long period the tape had moved from the centre of the rim slightly up onto the shoulder (or perhaps it was never fitted correctly) - anyway, the result was that I always had a problem getting tyres to seat on that particular rim, and the result was exactly as you describe, the tyres had difficulty in moving onto the shoulder where there was tape. The solution was to use an Exacto knife to remove the tape from the shoulder. Result - no more seating problems!

- Wil