This is not expected behavior. The 7344 should detect the index signal in either direction regardless of the phasing of the lines, as long as the polarity requirements are met. I would try this encoder on multiple axes to see if the behavior is the same or if the problem is related to just one axis. If it is feasible, try a different model of encoder to troubleshoot this issue.
Also make sure you have the latest version of the
Motion Driver, which is currently 5.2. Several rare encoder problems were fixed between version 5.1.1 and 5.2, which you can read about in the release notes.
Regards,
Brent R.
Applications Engineer
National Instruments