Hello, I have some more info for those who are interested. The problem occurs when using float figures and the caption goes after the image. If the caption goes before the image, then the figure imports ok, not great but ok. Unfortunately for me, IEEE transaction demands the caption to go after the image, so what I'll do is to have the captions go before the image for now and remember to switch them when the paper is submitted so at least I'll only have to do that once. Thanks to everybody and let people know that lyx is the best!
-Mario
