I dump with rawdump which gives an extension of .iso ... I checked my dump with the dat and it renamed it with the extension of .gcm. Doing that it shouldn't effect the image at all should it?
I believe that is correct. When I was dumping gamecube games, a gcm file was the same as an an iso.
.gcm extension can be used for shrinked images sometimes.
It is possible to "wipe" garbage data from gamecube games, which reduces their file size. However, it is still an iso. Also, if you wipe an image to reduce it's size, it cannot be read by a real gamecube. The gamecube console expects a specific file size, around 1.4 GBs I think, which is why dumped images will contain garbage data since they were padded to achieve the expected size.
Wiped gcm's can still be used in emulators, most of the time. Some games may play ok at full size and choke after they are wiped.
Realistically, the ".iso" extension should have never been. It's a direct reference to the ISO-9660 filesystem. It's alright I suppose if it were strictly for such filesystem images, but alas, files with the ".iso" extension often are images that contain filesystems OTHER than ISO-9660 (be it UDF, HFS, whatever) or non-standard deviations from the ISO-9660 standard (Joilet and/or Rock Ridge, or relaxations on filesystem limits).
I admit that I don't know much about GameCube discs, but I'd be surprised if they use good old ISO-9660.