How exactly did you check? Even if your hardware/computer is 64-bit, your OS may still be 32-bit. (This error can’t be caused by plugins.)
Version 0.1 of the game is 32 bits, version 0.108 is 64 bits.
There is one other possibility… which operating system are you using?
Edit: It seems that the update may be incompatible with Windows 7/8/8.1. I’ve contacted the devs about a possible fix that doesn’t undo most optimisations, so hopefully one of the next patches will work for you again.