Sync is set up to work from only 1 computer to Ancestry, not 2. You'll have to make a decision which is the primary computer and when you use the 2ndry restore the FTM files, media folder and sync control files (hidden in the Appdata folder) to the 2ndry. Then when moving back to the primary copy the files over again. PIA but that's how it is. I think some people have used dropbox for the files but I don't know for sure.
They're supposed to be working on this.