Sorry if this has been addressed countless times before, Tried doing a search for what I need but nothing came up.

Sometimes when I load my game up it appears that a few mods just decided to quit on me, and the elements of that mod within the game are obviously missing. As so far it seems the only way fro me to get them back is to deactivate the mod in Mod Manager and then re-activate it.

Any way to prevent this? I'm using the Steam-bought GOTY version of oblivion.

If Steam itself is installed in C:Program Files in a Windows 7 or Vista PC, it is probably UAC that is causing this. The solution is to install Steam into another folder like C:Games\valve\steam and then move your steam games into the same folder on your HD.
I hope this is your problem, but I do not use Steam myself.