I would like to expand upon this. I had started my day by wearing mark of the order (new monarch mark) but switched it to Mark of the six Fronts (rare titan mark). I had been leveling up the new Monarchs (lvl 1) but had recently switched back to a different mark to get my basic vanguard ranked up to lvl 2. I needed about 2300 to get there. Last night I completed several patrol missions 3 bounties and a few material exchanges. They all showed me getting basic vanguard reputation. Upon going to check in with my vanguard my rep had not increased, but it appears that my new monarchs rep had. So either just having a mark for a faction in inventory is forcing all rep to go to the faction or after equipping one it just fails to recognize it has been removed. Destiny app also shows the new monarch flag behind my character even though he is not wearing their gear as well. I don't know if this is a bug or an intentional thing but it is slightly annoying as I can't seem to increase my basic vanguard atm.