Instead of:
https://mega.nz/#!FILE_ID!FILE_KEY
new links have the format:
https://mega.nz/file/FILE_ID#FILE_KEY
This caused Megadownloader not to recognize the new links.
A manual workaround was possible, by modifying the links manually.
Version 1.8 has corrected this issue and now it supports files (and folders) in the new format.
It is already available, you can download the new version from the Download page.