Ok, I created a mod with two kinda new creatures, a skeleton edit of a sentry bot and a version of the "ZaksEye" with new animations. I selected it on the data list and loaded Fallout 3. First I tried to go to my Testing place I made that included the creature titled "aaaCETestingHall" by typing coc aaaCETestingHall. It just reloaded the cell I was at. So I moved the creatures to another cell that is part of the game already. I entered the place and nothing from my mod loaded...

If your CS and Game are patched at different versions, then the mod will be ignored when the game loads.
Fallout3 - v1.7
GECK - v1.5

Well I've had other mods load in the past while using the same game version and the same construction kit...
EDIT: Created a new plugin and loaded same files. IT worked