Implantation would by no means last for two weeks. It usually only lasts 1-3 days.
Your symptoms could be part of a larger issue, and although pregnancy is unlikely, it should not be ruled out. Implanon is very effective; but, of course, no method of birth control is 100% effective.
I would see your doctor. Firstly, some methods of hormonal birth control must be administered in larger doses for people who are overweight, since some methods are marketed for the "average" person. Secondly, it seems to me that your symptoms COULD be because of a hormonal imbalance. Or, maybe just your body expelling old blood (which is what brown blood is). Heavy cramps and back ache would also NOT accompany implantation bleeding.
Either way, this seems like a more complicated problem. The best advice I can give is to see your doctor. Good luck!