Check your TOC sizes. The SwapMagic DVD is 4.35GB. The Game shark is a CD, not a DVD. I think the AR is of the same design (at least it used to be). You need a DVD TOC loaded that is as high/higher then that of your backup for it to play reliably. If you are booting with a CD, it will not load a backup DVD. Bypassing the eject sequence does not reset the media flag from CD to DVD, nor does it reserve address space above the CD size so it won't even load the DVD files. You'll have to force a double swap method or get a Swap Magic set. For the cost/versus the headache, you may be better off investing in a soldered bootable modchip instead.
If it ain't broke don't try to fix it! But, hell if you can tweak that bastard just a little bit more....hehehe.