As always reference the LinuxCNC manuals and the LinuxCNC Wiki for more information.
Encoders
Index
The first thing to check when index does not work is index polarity.
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Run your Configuration
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Open Show Hal Configuration
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Find the index-enable for the axis or spindle and if it is linked to a signal, unlink it like this unlink motion.spindle-index-enable in the Test HAL command: box. Make sure you use the pin name for the axis or spindle you are testing.
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Software Encoder - In the Test HAL command: setp <encoder name>index-enable 1
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HostMot2 Encoder - In the Test HAL command: sets <signal name>index-enable 1
If the Value of the index-enable goes back to false immediately then it is likely your polarity is wrong.
If the Value of the index-enable stays true open the watch window and add that pin to the watch window. Slowly move the encoder through one turn and by the time you pass one turn the index-enable should be false again. If not check your wiring.