at work i work on 99% DC electronics. up to 7.0hp electric motors, 500 amp controllers, solenoids, on board computers. the works
and i know that the OBC (on board computer) regulates charging
if you think of it in a different light... while it is very annoying to not have 100% and the green light on the magsafe power adapter is on (meaning it's not charging).. your computer is doing what's best for the battery
for the most part, over voltage is bad. especially on something as important, and used as a computer battery.
if your battery was at, per say, 99.4% - there wouldn't be a healthy way for the battery to charge .6%. it would have to be on a trickle charge, and it doesn't make sense to do that for the computer battery, if it's .6% under charged.
it is healthier to leave it at 99.4% of total charge, than to risk over charging it. also if it DID try to go from 99 to 100% with that small of an increment - putting voltage to the battery to charge for split seconds (pulses) wouldn't be good for it.
what i usually do (to make sure it's ready for a full day of work, or a day where i know i'll be stuck at the airport) is leave it unplugged for a few minutes and it will go down to 95 or lower, and then the charging will kick back in (actually charging kicks back in even at 99%)
and it will usually goto 100%.
trust your machine, it's tryin' to make your battery last you more than a year!
p.s these are just assumptions about macs, im just basing it off of prior knowledge in another industry!