Last year, flying Copa, I had to connect twice at PTY on different tickets; once to CUN checking-in at SJO and then to MEX, checking in at CUN. The second checkin went smoothly, at SJO they were not able to complete it for both flights. A second agent plus a supervisor came to the desk to help, at the end they asked for apologies and I went through immigration and check-in at PTY. Mind you, I had two hours to kill, so I didn't care. The problem seems to be linked to pura vida...