I have not tried using .artx files created in older versions of Artisteer and not sure if there are things that may need tweaking in Artisteer after doing that. However I can say that the output from Artisteer 4 is much different than previous versions and you should use all of the exported files, you cannot use a layout.master from a previous version, its much different as is the theme.skin file. All of the files are important. Make sure you save the project in Artisteer to make sure it upgrades your .artx file format before exporting.
Older versions of Artisteer exported xhtml whereas Artisteer 4 exports html 5, it is much much different output, lots of changes in the markup. So it would not surpise me if some things got lost in the translation from an older .artx file.
Hope that helps,