You might see this message during the SYNC process if the databases get bigger than 1.2 GB (an arbitrary limit). The real limit is 2GB, beyond which Access databases dont work.
If the databases are too big (~1GB) soon after compacting (at the end of SYNC process), then its normal to see this message every now and then. All I can suggest is to use the (fantastic) interpolation switches to minimize the number of data points.
If the databases are much smaller after SYNC but this message still appears during SYNC then examine the scenario file that triggers this message. You can also try to locate tables within this file through the status bar messages on the bottom left side of the screen. Splitting large tables into several smaller ones will help as the databases are checked for compacting after each table.