According to a translation by Shih Tzu (one of the japanese->english translators for Cave Story), 126.96.36.199 has
* Reduced the CPU load.
* Expanded the 'Troubleshooting' section of the manual.
* Fixed the display of Naoku's picture in the manual.
* Added a sound effect for the Gravekeeper's attack.
* Added an effect for the Behemoth's charge.
* Fixed a bug in the Main Artery stage.
* Fixed a problem regarding processing issues on the title screen only."