Chests do not have a change in appearance when viewed through the semi-opaque part of a beacon. So far, only beacons appear to have this issue, as far as I can tell.
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From your new screenshot, however, It appears that the behavior has changed. Only one of the chests (or two, since it's a double chest) is rendering improperly, while the others blocked by the beam are shaded. Is it perhaps only affecting the one you're pointing at now?
Nope. It is not consistent. I just tried it again, and all the chests except for 2 were rendered improperly this time.
Different beacon beams actually affect the rendering of chests differently. That's an interesting observation.
Is this still a concern in the current Minecraft version 1.7.4 / Launcher version 1.3.7 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Is this still a concern in the current Minecraft version 14w07a / Launcher version 1.3.9 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Is this still a concern in the current Minecraft version 1.8.1 Prerelease 3 / Launcher version 1.5.3 or later? If so, please update the affected versions in order to best aid Mojang ensuring bugs are still valid in the latest releases/pre-releases.
Hmm... Does this still occur in the latest snapshot? The rendering engine has gone through some major changes in the 1.7 snapshots. My intuition is that the chest is rendering in front of the effect. Since the chest is a transparent block, this may be an instance of MC-9553.