Hello Nicola G and welcome to the forum.
I have had the brown discharge that you describe whilst on different types of HRT and I believe it is caused by the Oestrogen itself rather than the delivery method. Sometimes the brown discharge becomes more pink and has turned into spotting and then bleeding. I am in the process of reducing my Sandrena gel sachets at the moment so the most recent bleeding episode has stopped but I am now see the brown discharge instead.
I am sure that other ladies will be along with their comments but I think that your experience is very common when using HRT.
I hope this has helped you and wishing you well.
K.