frozen-bubble-client has the sdl patch not applied, because of the behavior of patch. I saw in the ebuild that frozen-bubble is symlinked to frozen-bubble-client. When now the patch is applied. The patch command moves frozen-bubble (the symlink) to frozen-bubble.orig (so the symlink is renamed) and makes a copy of frozen-bubble-client in the (now regular) file of frozen-bubble. So if you remove frozen-bubble afterwards in your ebuild _the patched file_ is removed. Make a simple mv or so as a solution.
Fixed in portage