excellent news! aynia, if you would list what the items were, you might help others who have a similar problem. *hint*hint*
Ok, it's been a while... but I know I deleted some custom trees - I'm pretty sure these trees were the reason the custom content didn't show when creating a sim.
General advice:Check your custom content (esp. objects), best to do this is in the build mode. There is probably something that doesn't work right and blocks the custom content to show up. Not working objects (also trees, windows etc.) are marked red (as far as I remember), or don't show up at all but check first for red marked objects and delete those.