The annotation issue is being cause by this join notation being used in the gbks. For example the line:
complement(join(4727880..4728107,1..738))
Annotation works if the join is removed. Making the above:
complement(4727880..4728107)
When fixing this, search the gbk on the keyword join to also find lines such as this:
join(4727880..4728107,1..738)
This line will also break table annotation.
Simply deleting the line from the gbk will make the fix.
Be aware that these "fixes" will cause regions of the genome to not be identified, however this should be a very small amount.