Water Softeners and Air Filtration Systems - Water hammer sound from water softener

I have a water softener made by Watermate industries with a 460 Novram Mp Electronic control system. The problem I am having is a water hammer or vibration from the control unit either between the brine refill and the final purge or right after the purge. I first thought it was the piping in the house but I watched it during a manual regeneration and found the top of the control vibrating. I have no idea what may have started this but I noticed my cold water had slight brown color the day after I first heard the sound. The ice cubes in the ice maker were brown. I did not notice any brown color in the hot water. I don't know if the city was checking fire hydrants that day because they claim there may be some brown water after the tests. If anyone has any ideas please let me know. Thank you.