The only thing I can think of right off hand is you need to "save" your rep if you are adding parts to it after creating it. In the bottom left corner of the screen, it displays the active simplified rep name, if that name has a plus (+) next to it, then the rep needs to be saved in the view manager, under the simplified rep tab. The modified rep will also show a plus (+) next to the name in that dialog box to.
Creo does this so you can make "on-the-fly" temporary changes to a rep that aren't automatically saved if you save the file. It has it's pros/cons but as long as pay attention to the (+) next to the name, you will know when (or if) you need to save your rep, prior to saving your assembly.
