I have been using WordPress Download Manager for a long while. I have never been happy with it but the latest update just makes me cry! If you haven't upgraded yet, don't do it! If you already upgraded you probably ran into the same problems I did.
All downloads gone - You have to go into the "Settings" page and migrate all your download packages.
All download icons are gone -Nothing more to do then go into each and every package and select a new icon.
Short codes like [wpdm_tree] doesn't work anymore - From now on you have to use a plugin, WPDM Extended Short-codes, for this. It isn't available in the plugin repository. You have to download it and install it manually.
All the links to your download list generated by [wpdm_tree] returns 404 Not found - This is true for both migrated downloads as well as new ones. This is probably because the new version uses custom post type instead of linking to the actual file. It works fine in preview but doesn't work live. This probebly has to do with permalink structures and so on, obviously not tested properly before release. I figures out that I had a regular post for each download with the link at the bottom so I just edited the permalink for each download to the same slug as that page. The result is that the user is sent to the post with the download link at the bottom that actually works.
I have been thinking about founding a new solution for my downloads for a while and now that time table was just pushed up! I hope some of this information helps you get through some of the problems.