Some EF lenses have 7 electrical contacts ("7-pin" lenses) and some are "10-pin" lenses (typically the later Canon telephotos).
Teleconverters such as Kenko's Pro 300 (and presumably Canon's own TCs although I haven't checked one lately to be sure) have 7 pins on the camera side and 10 on the lens side (actually 11: one of the pins on the lens covers two of the "raised" ones on the camera/TC). If you attach a 10-pin lens to a TC the camera recognises the existence of the TC and reports the effective focal length and aperture of the combination. If however you attach a 7-pin lens to the TC, the camera does not recognise the presence of the TC and reports the native features of the lens.
By covering the extra 3 pins on the lens side of the TC (either by using a small extension tube which only has 7 pins or by using tape as shown in the D30/D60 Tips section on Fred Miranda's website) you can fool the camera about the TC's presence. The main reason you might want to do this is to trick the camera into autofocussing when the effective aperture is above f5.6 (or f8 on some cameras). I have done this successfully with my 100-400mm IS (a 10-pin lens) and a 1.4x Kenko on a D30, although the AF performance at f8 is nothing to write home about.
This also explains why when you stack TCs the camera does not recognise the presence of the TC closest to the camera. Keep in mind that in situations like this the camera is not able to record the complete details about the settings used in the photo.