Just made the jump to version 3, and noted an issue. When I try to export all of my mockups as PNG images to a directory where I had previous versions saved, it prompts whether to replace them or save both. That’s good, but when I choose to replace, it actually creates new images with a “_2” appended to the end. For now, I think the workaround will be to export to an empty folder and then manually copy the files over and replace the originals.
Note: this was done on a Mac running Mavericks using Balsamiq 3.1.2