Some files on my oblivion mod manager come up as black, and when I activate them anyway the next time I turn on Oblivion they are deactivated again, most annoying.

I have tried the help and settings to try and stop it deactivating them but I cant find how to do it, any help would be greatly appreciated. xx

http://timeslip.chorrol.com/obmmm/index.html
this takes you to the read me.Read me's should always be read,before installing any mod,as some have special instructions in them!

I suppose you are talking about the omod being marked with a black box instead green (no conflicts) to red (potential damaging conflicts with another mod). The black one means Secure Serious Mutilating conflict with something. You shall not activate such mod unless you are sure, very sure what is going on. For the better, or quit installing the new mod or uninstall the former, conflicting one, before.

By what you says things may have gone mad at your setup. Don't rely on it anymore, uninstall and remove both mods (or more if is the case) and reinstall the one you really want.

PS: I mean it, deactivate the mods, the folders and files must be all messed by now, they "MUST be deactivated, both, by effectively clicking the Deactivate button. and only the desired one shall remain in the list, the other shall be removed for good, to avoid being ever activated again.

I think a small explanation will help understanding what happens. The omod at the right window have nothing to do with the game, it not even is into the /data folder (commonly it is into the /mod folder into the /obmm). When "activated" the actual files are installed in the correct places, and removed when the omod is deactivated.
This is a physical act, when 2 or more mods shares the same files, the last activated mod will overwrite the files existent. Worse, removing any mod from a group that have shared files, ALL mods loses these files and so the remaining mod MUST be reinstalled (if no omod) or activated AGAIN if is a omod.
This is not a problem with OBMM, it happens whatever the files are removed by OBMM or by direct action from the user, and the same procedures applies.
Remember, unless you know for sure what mod was installed later, you can't know if the files there are the corrects for the "'de fato' active (last) in the load order" (at the left window) or if it is using the files of the last installed (from the right window).

This shall be understood once forever: The files at the right window in OBMM have no meaning at all to the game engine! They are exactly the same as any and all "mod 7z files" you download somewhere, waiting to be installed (this is a general answer not meant to anyone in particular).

file in the OBMM's right window, with a blue mark just tells it was installed sometime ago, and thus, have it's mod actual files installed (hopefully, if the user didn't messed things).

What do brown ones mean?

From the FAQ section of the read me. (You really should read this)

The omod list:
The right hand panel lists the currently available omod files.

The coloured square next to each mod indicates its status. Blue mods are currently active, green are inactive with no conflicts, orange are inactive with minor conflicts, red are inactive with major conflicts and black are inactive but activating them will overwrite an esp belonging to another mod. Holding the mouse pointer over an omod will display a tooltip containing some info about the file as well as the mod description. If you want certain mods to stand out, you can assign them to a group and then set a different font for that group.