I don't know what type of indexer you have - mine is an optical refector - but whatever it is, the information is available on the diagnostics page.
If you turn the spindle, you should see the indexer "led" flash. I must assume , from what you say, that you are satisfied that this is working.
1. Check, if you can, that your indexer is "working" at the spindle, then at you BOB.
2. Check your have the indexer properly configured on the Config/Ports and Pins/Input signals/INDEX (not timing) pin. If you are getting an incorrect reading - i.e. off when on, etc - click "active low" - check it is enabled with the correct port and pin number.
3. If you are getting the indexer showing on the diagnostics page, you might check the debounce settings on the General Config page and adjust it to get the best result.