I've gotten around the floor limitation, by using columns. Technically you only get two screen shots per UPPER level. So a one floor house will get two images, and a one floor plus 3 basement house will still only get two images.
BUT! If you use columns, you can trick the lot into thinking it's more floors. Lots of things count as columns, including the roller coaster supports, the castle tower pieces, the circus tent pieces, and the Mill chimney pieces. So you can have a really tall chimney, and for each height above what the house is, you gain two extra images.
That's the only way I know how to do it. Maybe there are other ways that other people know that I don't, though. A two story house with 11 UIC images certainly indicates that there are better tricks than the ones I know.
I've never had a problem uploading something after using UIC on it, but maybe there was something about those images. Were they jpg, png, or something else? I generally use png format, but I think jpg should work fine as well. If you use png make sure you flatten the images and don't leave any transparency in them. That might make the launcher hiccup, for all I know.
ETA: Oh! Do you have a link for the lot in your studio? I'd like to download it from there and rec it for you. :)