The reason for the difference that you see is that Smart Matches™ are not fully synchronized yet between the Family Tree Builder software, and the family site. Even if you are using Family Tree Builder, you are encouraged to use the new Enhanced Smart Matching™ on your family site, and enter new information you learn using Family Tree Builder.
FTB SmartMatch cannot be started until the tree has been published. After publishing the resiults differ in FTB and in the published tree.
Why not use the same basis?
In my example the only difference is that I'm missing 1/one tree with 13 matches. Every time during the last 3 days that have been the only difference when refreshing. This is not an co-incidense - this seems to be an error.