I have the Metra Axxess controller with a Pioneer X930 HU and it works.
There are settings for the Axxess for Seek up/down and Preset up/down. You probably have the toggle set for Preset. This will allow you to cycle through radio stations and albums or folders on CD/SD cards but not cycle through CD tracks or tracks within a folder on SD/USB. To cycle up/down on tracks, you need to change the toggle to Seek.
The problem then will be that you can't cycle up/down through radio stations. You will be Seeking through every station and not your presets. To get around this, I use the toggle for Seek and programmed the on-hook BT button for Preset up. That way I can at least cycle through radio stations in one direction and I can also use that button to switch to the next folder on an SD card or next album on an ipod.
Hope that helps. I can't offer any advice on why your ipod isn't working.