The cymac3 internal clock was off by about 10 seconds. When I tried to start the NTP service, I found out that the cymac3 couldn't reach any external server. It turned out that the gateway in /etc/network/interfaces was set to the wrong address. I fixed it and rebooted. Now NTP is working and the time is correct.

This fixed a small issue with diaggui, which always complained about a data receiving error when starting a measurement (although after the complian the measurement could continue)