As in the topic title: GenBank annotated files fail to load if there is one or more annotations defined using join() vector which has elements not given in ascending order (CLC Workbench exporter can produce such files). Changing the order manually in a text editor makes such files load just fine (at least on Windows).

My bad, there is a rather nonsensical annotation artifact from CLC Workbench in the same file which causes the problem:
Code:

join(1221^1222,complement(1221^1222),complement(1221^1222)) 

Removing that entry makes the file load fine with any element order in join() vectors.