This just happened to me today. I put my phone on the cradle every night and then take it off every morning. I know that by lunchtime, I will be around 70 or 80% and usually end up around 60% at the end of the day. Today at lunch, it said I had 5%. I put it on the cradle for a few minutes and when I took it off, the battery was at 60%.
Apparently, a glitch. I'll buy the re-calibration story.