The One/Four Phase button needs to be changed along with some switches in IR6. The module of interest is in the HER VXI crate (upper right), and contains the switch settings for both LER and HER. LER switches are at the top and HER switches at the bottom of the module. The switches of interest are the B0 and B1 switches. The left position means free running, the middle position means a solid "1", and the right, a solid "0". The B0 value determines the setting of the 0-180 phase switching, and the B1 value the setting of the 90-270 phase switching.
The Four-Phase software setting corresponds to both Free Running (left), and the One-Phase setting corresponds to both a solid "1" (middle position). The other settings are for diagnostic purposes.