FAB 3000 does try to optimize/verify every imported gerber file (because Gerber files are known to have invalid polygons, duplicate data, etc); whereas ODB++ are generally more efficient and can be directly imported without optimization/verification.
Note: Does the gerber file use "thousands of hatched lines" to fill-in a solid metal areas? If yes, these could be a cause. Feel free to submit a support ticket and send us any set of gerber files that imports slowly, and we'll be happy to immediately determine the cause. All customer data is treated confidentially and deleted after support incident is resolved.