From your description, I would almost suspect ring end gap is too small. Once the motor warms up a bit, the rings close tighter due to expansion. IF they're too tight, then they are causing a seizure in the cylinder. Engine cools, rings shrink, and the cycle repeats.
Can you confirm you properly measured the gap prior to installation?
If its not this, then I would replace the condensers and verify fuel level (bike starves for fuel due to improper float height or function). I'm leaning towards my first diagnosis though, as the problem pre-existed the carb rebuild, and afterwards.