I think your discolouration is almost certainly caused by iron. You only need a trace amount of iron to cause an orange-brown rust colour which can make it difficult to confirm by analysis.
As this discolouration is new, it indicates that there is not a problem with the system design (saturator) or the softener water quality. It appears to be caused by a recent change – either using new pipework containing old water with iron in it or a one off issue with the sodium fluoride quality.
If your product water meets the required drinking water standards and you can live with the aesthetics of brown stains in the saturator, you may chose to take no corrective action (other than continuing investigations and confirmation) alternatively dissolve the iron using a solution of citric acid/EDTA – discharge this batch of fluoridated water, and the next to waste.