I found an article that looks like it applies to your situation:
Mac notebooks: Battery may not show a full charge in Mac OS X
It notes the following:
Some Mac notebooks (MacBook) may not show the battery as 100 percent charged in Mac OS X, even when the power adapter is connected. The battery may appear to stop charging between 93 percent and 99 percent.
This is normal. The batteries used in these computers are designed to avoid short discharge/charge cycles in order to prolong the overall life of the battery.
When setting the Mac OS X battery status menu bar icon to display charge state by percentage, you may notice that the reported charge stays between 93 or 95 percent and 99 percent.
The adapter will not charge the battery to 100% automatically if it will add additional wear to the battery.