I had a student who tried to use Ultiboard for a project. The project required a custom footprint for an IC. When he sent the files out to a board fabricator, they replied that they couldn't handle the Gerber file.
On examination of the Gerber file, I saw that Ultiboard used HUGE multiline macros for the custom footprint. I've never seen such long macros - and apparently the board fab house and its software supplier hadn't, either.
So you need to check with your board fab house to see if they can handle the files. (GerbView could, by the way, so there was no advance warning of problems).
--fred