When you reload while in the sitting position, it triggers the standing up animation for a short moment. Additionally, if you have your sidearm equipped, it will reload an invisible sidearm.
update May 9th 2013:
Animation glitch for Primary Weapon is fixed in version 0.56.104.778.
Reloading sidearm while sitting still results in reloading an invisible sidearm plus some minor glitching of the primary weapon.