This is typically caused by the following:
1. An editing session has not been started in ArcMap. To activate the check-in tool, on the ArcPad toolbar, an edit session must be started.
2. This occurs if a shapefile is being checked-in; the check-in tool can only check-in geodatabase feature classes. However, it is possible to check-out a shapefile but not possible to check-in a shapefile. ArcPad check-in/check-out tools are designed to be used on geodatabases feature classes.
The best approach to export a shapefile is by copying it over to a mobile device using Active Sync. Then copy it back using Active Sync, replacing the original shapefile, to preserve edits done to the shapefile while in ArcPad.
3. The ArcPad check-in tool may be grayed out if the geodatabase feature class has already been checked-in. Feature classes can only be checked-in once per check-out.