The first step in resolving this problem is to get rid of the duplicate playlists. This can be a time-consuming pain to do "manually" deleting playlists one-by-one. To speed things up, you can launch Automator on your Mac and select the Remove Empty Playlists action from its Music Library. Alternatively, Doug Adams has that will do pretty much the same thing. Even simpler, you can purchase Mr. Adams' utility ($1.99 in the Mac App Store) and delete empty playlists with just a click.

If your duplicates are not empty, you can create an AppleScript that will delete all copies of a playlist of any name you specify. An example script for doing this is posted in the above-linked Support Communities thread.

Next, to hopefully prevent this from happening again and to bring back any non-duplicate playlists that may have disappeared at some point, select "Update iTunes Match" from the Store menu in iTunes. If this doesn't work, try the same fix noted in the previous section: Turn off iTunes Match, while holding down the Shift or Option key, and then turn it back on again. If you do this, Apple recommends that you first disable iTunes Match on all of your iOS devices and then re-enable it on these devices after re-enabling Match on your Mac.

If none of this works, check the above-cited thread for further variations on these suggested fixes.