The problem of "one link" is fixed in 0.6.3. The root cause of the issue is the square brackets generated by the plugin as it interferes with JIRA wiki syntax.
Before: Build is scheduled for: [http:After: Build is scheduled for: http:
The "two build URLs" problem seems to be caused by Jenkins not notifying the plugin correctly. This issue can't be reproduced now but can still theoretically happen. The workaround is to restart Jenkins. Please reopen this ticket with all of your Jenkins details and logs if this is still happening.
This problem has happened in the past for pipeline job as per seen in this commit.