Anyone Have Problems With Seq3 Midi Sync?

Has anyone had issues with Seq3 syncing to external clock? It shows the correct BPM synced but every time I go to record a new sequence and I complete the recording by hitting the AUX button, the sequence starts about an eighth note or quarter note late (hard to tell exactly how late). If I pre-record a sequence, it usually starts on the downbeat correctly. Ideally, I’d be able to record sequences live in-time with the external midi clock and in perfect sync, but I haven’t been able to get live recording to work.