my instinct tells me that you possess two fantastic pieces of history there, but you might have a lot of difficulty proving it!
I would concur that the red ensign is most likely naval, and judging from the size of the other flag, that is most probably naval too. Neither would appear to be Regimental in any way, and as far as I am aware, no colours of any description were taken into action at Majuba.
Furthermore, I have never personally read an account of the battle that mentions any form of flag being flown, carried or captured.
Given their apparent size, they would appear to be 'jackstaff' flags. Pure conjecture, but I wonder if they did indeed belong to the Naval Brigade and were intended to be used to mark specific points at the top of the hill, such as a command post or ammunition point? Also, the Naval Brigade was deployed in 2 sections once on the summit, they could have been used to denote their positions......
I would suggest looking at the naval angle as your first point of research, but I'm afraid that the only naval reports that I have personally seen are the ones contained in the London Gazette dated 3.5.1881 by Lt Ogle and Dr Mahon RN. There is no mention of any flags.