Items disappear in Creative Mode inventory

I created a superflat world with a custom preset that generated a layer of locked chests. I made a couple of hopper clocks and hooked one up to a command block that would clear my inventory of item frames (ID=389 (What I wrote into the command block= clear @a 389)).
The strangeness was, it deleted everything that I pick up on mouse click. When I put the items down however (before they are removed), they are not touched by the constant clearing (and I understand what the clear command was intended to do). So I tried relogging and destroying the clocks, and relogging again. Nothing would quite work. After turning on touchscreen mode and experimenting around, the error stopped. It began again when I turned touchscreen off. I even forced an update and tried to play offline.
I downgraded back to 1.5.2 and the problem was solved (but the game closed without a crash report a few minutes later), and as soon as I updated again to 1.6.1, the problem persisted once more.
I tried surfing the web for an answer. I allowed myself to think that I was the only one with this annoyance—as there was no way an update so new had many people discovering its bugs.