In one of the setting boxes, there is a tick box for TrackMate compatibility. Clicking, or clearing this used to sort my problems out.
You can also check the IR downlights using a Digital camera or similar. You will not see much light, but you will get an indication that they are on or off. If you are running under certain lights or sunlight, this can trigger sensors, or prevent them from working. Make a shade/ tunnel over the sensors and light bridge.
Also, check the debounce is not set too high.
andy