Like KennyR says AGA is only enabled by Setpatch. To run some AGA demos from "no startup" you have to run Setpatch first for the same reason.
Maybe something you installed has overwritten with a Setpatch from its archive, you need OS3.0+ Setpatch for AGA. Compare the versions of Setpatch on your HD with the one on the boot floppy that enables AGA OK, if the one on the floppy is later copy it to your HD.
