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The gray icons are unfortunately a new feature and not a bug - Since Aperture 3.3 are the icons drab and gray - the Aperture 3.3 Release Notes are calling this:
Newly designed monochrome source list and toolbar icons.
The Release notes will tell you, what has changed since then:
The only way to change it, would be to manually replace the icons by colored ones in the Aperture application itself. You would have to patch the application bundle and to exchange some of the tiff files in the "Resources" folder.
And each time there is an update you would have to start over.
There are quite a few discussions on this, see:
P.S. Some hand colored icons to replace the grey ones are here: