Hello Francesca,
Thank you for the bug report. I have fixed this bug.
Uploaded Java wrappers have the version "1.1-beta6-pre3". You can
download them from this page:
http://ggasoftware.com/download/indigo_next
(Java wrappers points to an updated version, while all other links
points to 1.1-beta5 version). Official announcement of the next
version will be done later.
Also in this version "not atom list" is also saved into molfile
properly. It wasn't so in the previous version.
Best regards,
Mikhail