It is most likely caused by autosave. Autosave saves your changes to the RapidWeaver project file whenever you Quit. It also saves when switch to another application.
This is a handy feature when you're working on a small-medium sized file, however if you're working on a large RapidWeaver project the save may take a noticeable amount of time and things will stall until the save completes.
If you are working on large files, you can switch off the autosave feature in the RapidWeaver preferences.
- Choose Preferences from the RapidWeaver menu.
- Uncheck the checkbox labeled Enable Autosave and Versions.
- A dialog box will appear, click Restart Now.
Remember: RapidWeaver will no longer save your work for you, so make sure to Save as often as possible.