I ran into the same issue and it looks like that with the 9.6 update they "broke" the way that static sync and $nogo works. If you use the full path of the folder then the folders will be ignored. If you want to go back to the previous behaviour where folder names are matched (and not full paths) then you will need to edit the source code. The fix I am using is as follows:
1. Open this file:
/pages/tools/staticsync.php
2. Add this at line 273:
$nogo_folder = basename($fullpath);
3. Edit line 276 to be:
&& strpos($nogo, "[{$nogo_folder}]") === false
Scott