Can't say that I've ever had that problem except when checking the "Use View as basis" box when exporting. When that box is checked the multiple file export has done a few funky things on me, much like you are describing. The best solution I've come up with for that is to leave that box unchecked and just export with 0 percent overlap and a fairly high image resolution (i.e. somewhere in the 1024 range). The only problem I've found with that is that there are, on occasion, seemingly beveled edges to the images which can be a pain when trying to merge them. Waldonrate is, however, the resident expert on FTPro, so perhaps he'll be along to take a look at this thread and offer some more info regarding your problems.