I am developing for Google TV, and using Flash Builder, if I set my resolution to 1152, 648, go to the SWF on Google TV, it is way off the stage. If i do the exact same dimensions in flash, it fits PERFECTLY. Why does flash builder and flash handle the stage differently and can I make Flash builder work like Flash.
I'm not sure if I have the answer to your problem but it could be the way you are placing or creating assets.
Typically, in Flash the "registration" point of an item in the library is in the middle of the item so if you were to put the item at 0,0 for example, it would be half off the stage at the top and bottom. Flash Builder, I believe, handles registration points at the 0,0 point of an asset. As such, if you have created your layout in Flash and placed things based on the middle registration point everything in Flex would appear "shifted" down and to the right.
Again, this may not be the issue but just something to check.