The only time we've seen anything like this is when some other application doesn't play nicely with the tracker overlay. The best way to troubleshoot this would be to close any apps that may be running one by one and try again, especially if they have overlays themselves. Make sure to restart the tracker software (just to be sure) between tests.

You should have the tracker running before running Planetside. This isn't required, but it should always be seamless this way. Let me know when you find out what was conflicting.