To start out with we don't have any screenshots of what you are doing so nobody has a clue.
In the video that shows how to use the fpsc entity maker there is a section that shows how to import characters and I believe you have to make some kind of correction...I haven't imported a character with it for a while.
And just because your modeling program shows you character standing doesn't mean that the entity maker will import it that way.
I use Milkshape and some of my entities get imported backwards, upside down,etc.
Post some screenies and give us some more info and maybe we can help.
We just don't have enough info to go on at this point.
