I just bought the program a few days ago and have had the same problem. I did my laptop first. Finally I deleted and unsynched both so I could synch with desktop.
It appears that the only synching is with one computer and ancestry. I can not see the utility of installing a second copy of FTM if that is all synch does. The second installation will have no utility since any changes performed by that program will not synch.
The advertising and help are misleading since they both imply that you can download from ancestry and then synch on another computer.
If your primary computer dies you will still need backup since you won't be able to download from ancestry and link.