Using Linear position controllers is not recommended because they can produce invalid position data. This can cause the character or part of the character to disappear as the bones in the reference pose shoot out into space. FaceFX Studio 2009 recommends linear position controllers in the log, but Bezier or TCB are now the preferred position controllers.
To switch controllers, select all of the bones in the Reference Pose, then issue the following Maxscript commands:
for obj in selection do obj.position.controller = Bezier_Position()
for obj in selection do obj.rotation.controller = Bezier_Rotation()
for obj in selection do obj.scale.controller = Bezier_Scale()
TCB controllers are also supported.
As a bit of background, the FaceFX Max plugin can not write data to all controller types. Reading data works in all cases, but writing data to the controllers is only supported on TCB, Linear and Bezier.