"Download genbank format file" produces invalid genbank whenever a feature name is over 15 characters in length. In this case the feature interval is appended directly to the feature name with no space in between. The file then cannot be imported in to other software.
http://flybase.net contains many feature names which are over 15 characters so practically anything exported from Gbrowse on their website is invalid.
See line 26 of the example file invalid.gb