This happened to me the other day and I scratched my head, I just loaded DiskImageGUI, double-clicked a device and loaded the ADF in that way.
Side comment, even though the icon for the DiskImageGUI tool is present in the usual location it strangely isn't appearing in the Workbench window :S I use the Find tool, search it and double-click it that way.
However ADFs are somewhat irrelevant to me now as I registered WHDLoad, no slow floppy disc loading! It works perfectly within RunInUAE!!! Amazing work Chris. :)
I can now understand why someone is eager to get a PPC JIT working - some AGA games are dog slow especially Pinball Illusions. Not having hardware composition drivers probably doesn't help either - but after all that ranting I am suitably impressed. Boy I never remember Project X being so hard