I just noticed again how two auto tags, both one second long, combined with automatic gap filling, can mess up time tracking. I hope this will be implemented.
If you have access to a webserver, you can use a custom timeline as a workaround. You'd need to have a script accessible via http that return the csv data in ManicTime format: http://support.manictime.com/knowledgebase/articles/686418-custom-timeline
I use this solution for calls. All call logs are imported to a database that ManicTime can acces via a php script.
You can do this with the Manictime Server.
Set up the server on your desktop, log in both ManicTime Clients as the same user and then you can add remote timelines on both machines.