Go to Options (menu: Setup / Options...) and select tab "Default Values". Uncheck the option "Export Arcs (when possible)". Your gerber files should then export fine.
Note: During Gerber output, the Export Arcs feature goes though each gerber file and estimates where arcs can be replaced (instead of line segments) to optimize and shrink the Gerber file sizes. My guess is there are traces with duplicate points (or zero length) that are confusing FAB 3000 when adding additional arcs. You can try adjusting values for Arc Detection Tolerance and Minimum Chord Angle to help import results.
For additional assistance, please submit a support ticket and include both the original Gerber file and the one after export.