Version 2.1.0 for Windows and Mono is up. It adds node refresh on folder, region, and NBT file nodes, which has been requested a few times now.
The program does not save my changes. I have a chunk error with 16.656 pieces of cobblestone on the ground which has broken my save.I managed to find the chunk and manually deleted 1000 entries, but if I close and re-open, the changes were not saved.
Try editing a normal value (you don't have to actually change it, but press okay to commit it). That should prompt the editor that something is modified. Maybe that state just isn't propagating correctly for deleting values.
Edit: You should edit a value in the same chunk, as opposed to something unrelated, so that the chunk and region get rebuilt.
You need to give me much more specific information. What error? Take a screenshot if you're unsure.
Other than that, make sure you have .NET Framework installed, either 2.0 or 4.0 should be okay. If you're on XP it's possible you wouldn't have either, but you should have one of them if you're on Vista or 7.
A new version 2.2.0 is available, which fixes the delete/save bug reported by Evil Hamster, and also adds multi-select support. Currently only the delete action is available with multiple nodes selected, but other actions may be made available at a later time if it makes sense.
As with all bumps to the middle version number, a significant feature has been added, or a significant change has been made to the underlying code, both which entail risk. Previous versions continue to be available on the GitHub page for this reason.