You were right - for some reason I typed HWPWN instead on HPWM, so I couldn't find it in the 2.6 manual. I have always configured by hand, and have never used this command. I also always use 10 bits.
I still recommend checking that all the configuration is correct. I have also seen issues with low frequencies on this device. Why not set it to 2K to test that's not the issue here, just to eliminate that possibility?