Yes. It's happened a lot to me recently. I dropped over 100 points from my bullet rating from my clock draining away.
For me, it's from lag. I have a wireless modem and sometimes weather conditions affect my internet. Also, whenever my computer is downloading automatic updates, it lags my connection as well.
The worst is when I'm premoving every move, and my clock is still draining away 2 or 3 seconds per move. :D
Check your connection, and/or any downloads that may be happening in the background, is my advice.
Best of luck!
I have noticed on several occasions chunks of time being taken off when i blantantly havent used it. Has anyone experienced the same and why does it happen? (im not a sore loser this is genuine)