This will happen if you setup sonar as a timing slave via the MIDI sync option in Sonar. When using this mode Sonar will record audio but not necessarily keep the timing correct.

A potential workaround is to reset Sonar's clock source to "Audio" and then in the Sync tab select Sonar to "send/Transmit MIDI start/Continu/Stop/Clock/ "so that Sonar is now the MIDI clock master. Change your Sequencer to then respond to an external MIDI clock.