Most of the time, the message is accurate. Somebody modified the file in Microsoft Access. The error is actually just a warning message. If you added spec records on the fly (manually), you'll lose those changes when you rebuild the spec in the Specification Generator.
However, here is another way this could happen.
When you open a spec in SpecGen, the application will do a quick check between the physical modified date (stored in MS Windows) and compare it to the time written inside the Spec [Table: SpecInfo]. If there is a difference of more than 30 seconds then it will prompt you with this dialog.
So, based on what SpecGen is doing, you could probably guess that if your date and time settings on your local machine are different from the server where the specs are located (even by just a minute), you're going to get this warning message every single time. Also, it would happen if your are in another time zone and need to modify the specs in SpecGen.
The message itself can be ignored if you do not modify the specs directly in MS Access. But, if you really want to get rid of the message, sync up your local machine's time with the that of the server.