USB MIDI sync is only as good as the signal chain. If you are connecting your FLXS1 to your computer through a USB hub, or through another USB device, you may experience latency. This will be most apparent during recording, as the tracks being sequenced by FLXS1 might be up to 50ms delayed compared to other tracks. If you are experiencing this, try connecting FLXS1 directly to the USB ports on your computer and try to record again.
FLXS1 should have 0.5ms - 1ms of expected latency (well below the 1.5ms acceptable latency in the MIDI standard) when syncing over USB.