Perhaps you added something really large to an entry? Caboodle currently has to write out every entry when it saves (manually or automatically when changing entries), so a lot of large attachments will slow down the write times.

Have a look at your recent additions and remove anything really big. You can store it in a folder in the Finder and alias it to Caboodle instead, by dragging it in with the Ctrl key held.

In a future version I'll change the data storage to be more efficient, only writing out the changed entries.