When using the intelligent scissors tool, but not completing the polygon, the selection will remain active if you switch to a different a different tool such as the rectangle selection tool. After doing this, the rectangle tool will still work fine, but there is a ghost image of the intelligent scissor tool while it is still trying to close its polygon. If you switch back to the intelligent scissor tool it will allow you to complete the polygon you started.
Photoscan Standard 0.9.1.1684
Windows 8, 64 bit