Why does my Macbook Pro destabilize after hibernation sleep?

Question

Over the last several months using Mountain Lion, I decided to completely drain my battery to reset it. I think it then goes into what is called hibernation or emergency sleep mode. I am usually unable to wake it from sleep prompting a forced resstart.
to restart, I connect the adapter and the light goes green quickly changing to amber as expected. After the restart, however, some top menu items are missing such as the wi-fi icon and the Lock Keychain icon. All third party icons display correctkly. The space is there but blank and I can access the pulldown menu by clicking in those blank areas.. When double clicking the HD icon in the Finder, no icons show on the left side any more. A restart does not fix the problem. The system then eventually destabilizes to the point that I have to restore from my Firewire external HD clone using SuperDuper. One time I did a full restore (that takes forever even with a very fast wi-fi set up) to fix the problem.
I am usually in Safari or playing a Game such as a third party card game application to pass the time until the battery completely drains. I also have Filevault enabled.
Why is the MacBook Pro battery reset causing this OS instability? How can I reset the battery without encountering these sleep issues?

Answer 1

Thank you Dale.
This article mentions that recalibration should be done every two months. I think I waited 4-6 months before doing a recalibration on purpose. Though I probably ran out the battery power before then recharging overnight (some commenters on Apple Discussions said to wait 5 hours before recharging!).
I think that my battery goes into a forced shutdown rather than true sleep. Your linked thread states that this often causes directory damage. But I ran DiskWarrior and Disk Utility immediately after the stated problems occurred. And these programs pretty much repair any directory damage. But they failed to correct the problems I listed in my original post.
So I question the conclusion that not calibrating every two months caused irreparable directory damage that even DiskWarrior or Disk Utility cannot repair. The damage appears more extensive than this in my opinion.
The battery is only a year old with 92.35% of its original current capacity and 537 cycles. The current charge is over 6350 at 99.47%. It will eventually go to 100%. I can run over 4 hours of normal usage on a single battery charge.
Side note -- to my knowledge, nothing in the original MacBook Pro manual suggests that the battery requires regular recalibration of any kind to maintain the integrity of the battery. Much less every two months. If this is a requirement or even highly recommended, then Apple has done a good job hiding this information. And the available recalibration information varies from one type of battery to the next and is often inconsistent.
Apple's comments in the past support the idea that recalibration improves efficiency and fixes some battery issues as they occur, but that it is not manditory to maintain the health of the battery.
Do you have an official battery recalibration source (preferably Apple) that indicates regular battery recalibration is crucial and exactly how this must be done for MacBooks with builtin batteries?