had this happen recently, I needed to install some updates... and then it happened again, just had to reboot and the problem went away. Saving it as an EPS always seems to work better though, as .ai file susually only import what is on the artboard versus everything on the"whole page".
If you have Illustrator, it should be a slam dunk to open the AI there, and re-save as an EPS to get it over to FlexiSIGN. If you do not have Illustrator, or CorelDraw or similar, your copy of Flexi (6.5) is roughly 11 years out of date, and will not be able to open any of the newer versions of EPS, PDF, AI, or a host of other file types that have been created in the past decade or so. In that case, you might want to upgrade your software to a more current version.