Like the others have said, do it in your video editor if you can. Much easier.
But to address the actual problem you're having, it might be due to a discrepancy in the pixel aspect ratios. Not being familiar with the software in question, I can't go into more detail, but to give an example, if you drop an image (which usually has square pixels) into an NTSC widescreen video project, which has pixels 1.21 times as wide as they are tall, the image will be stretched. Check out the settings of the two clips and see if you can find anything... maybe other users who use iStopmotion can corroborate this theory and provide more information.
StudioL30's solution is not a good idea... unless you know the exact ratio by which the image is being stretched, you won't be able to get the proportions exactly correct... and more importantly, it's treating the symptoms and not the disease itself.
With all due respect Noodle, I don't want you here. - Ratboy Productions