I had the same problem with a SX30IS a SX100IS and a SX40HS. Pictures taken in auto focus are sharp. If I use the Canon manual focus at infiniy or auto focus at the moon, it willbe out of focus in manual mode. If I look at the EXIF I get the same value.
Since I got that problem on 3 different camera I suspect it is a common problem not senn because few people une manual focus.
The picture of the moon included show the difference before and after with a SX30IS.