- A 32-bit version of the game was added, providing performance improvements for 32-bit operating systems. The 16-bit version remained available for compatibility with Windows 3.x.
- A new help feature was added, providing assistance to players who are stuck.
- Minor changes were made to some areas. For example, color-changing mushrooms were added to Shelter Rock.
- A link to 'Practice Mode' was added to the map screen (previously the player was required to press the keyboard shortcut CTRL+P in order to use Practice Mode)
- The rate of advancement through difficulty levels was slowed, meaning that players advance in levels after three successful passes through a leg of puzzles instead of one pass.
- The save game format was changed slightly. Saves from v1.0 are compatible with v1.1, but not the other way around.
- A brand new executable was written for the game, using DirectX rather than QuickTime.
- This version is only available as a 32-bit executable.
- A number of new mouse sense features were added.
- Added credits, including a list of our supporters.
- New illustration and animation for the final road to Zoombiniville.
- Bug fixes:
- Fixed rare issue where the game could not be completed.
- Fixed bugs in Mudball Wall, Titanic Tattooed Toads, Fleens, and Mirror Machine.
- Optional on-screen captions in English and Spanish.