I’ve noticed when I use polyurethane caulk on exterior butt joints of wood siding ( particularly cedar siding ), and then prime and paint over it ( oil or water base primer, water base top coats ), after a couple of years all the caulk joints are visible. Is polyurethane caulk not the right caulk for this purpose, or do I simply need to seal it better before top coating, maybe using a couple of coats of a stain locking primer. Has anyone else seen this problem?

Caulk only has the ability to stretch and compress so much. After a few years, just about every butt joint on exterior siding will be visible and will need to be recaulked and repainted.

I understand what you mean. My impression has been that polyurethane caulks last much longer than latex caulks in the way you talk about - they remain flexible longer. But they also seem to show through the paint much sooner than latex caulks. Maybe there is something better than either - any comments. Thanks.