yes, there are size limitations to everything (that i know about) in flash. with objects that are masked you start to see problems when one of the dimensions exceeds 2880 px.
If your talking about an image that has been coverted to a movie clip symbol in flash, and not an actual movie clip like flv, mov, avi, etc. you could try just breaking it up into 13 pieces of a 1000px (or 26 of 500 etc.) then just add the next image to the stage with a frameEnter event or the like when scrolled to.
you'll hit a problem with masking as the masked object exceeds a certain size.