I'm having this problem but it doesn't seem to affect the play world, only inventory right-clicking. That is highly annoying but means I can still play creative ok. It seems to only be happening in 1.6.1, 1.5 was fine regarding this issue.
Maybe this is unrelated, but since I got the new launcher in 1.6.1 I've been experiencing a glitch that cause right-clicking to not work in the inventory on my mac. I have a OS X 10.6.8, and I thought that because it won't use the most recent version of Java that might be a contributor. With the previous launcher/version, the only way to right click in the inventory would be to use the key assigned to that function, which would work only with a click and the key together. However, when placing blocks and interacting (i.e. pushing buttons, etc.), the key alone would suffice. Now I'm using the new launcher in 1.6, and while the normal world is still ok (I'm currently playing creative just fine), the inventory right-click will not activate.
I had a similar issue with a disappearing block in 1.7.4 on the boundary between a tundra and extreme hills edge biome. Not sure if that's relevant, but I was using an efficiency IV diamond shovel on dirt when it happened. I was in SSP running on a MacBook.