Nope. It is not consistent. I just tried it again, and all the chests except for 2 were rendered improperly this time.
13w42b: Bug still occurs in the new rendering engine.
This bug still applies to the latest version of the launcher and 1.5.2. The bug never applied to 1.6.1 or 1.6.2.
This occurs for me in 1.5.1. It seems to occur only when the animals are crowded and the chunk is loaded. I have yet to observe it in action, but it only happens when the chunks are loaded and the animals are under pressure. It's also not just transparent blocks: I've tested it with glass and cobblestone with identical results.
Different beacon beams actually affect the rendering of chests differently. That's an interesting observation.