Having
/.gvfs in your Exclude Filter will only exclude a .gvfs-file that is in the root of your left and/or right base-location, not if it is in any of their subdirectories.
You need to enter either the correct path in front of
/.gvfs, relative to your left-and right base location, or enter
*/.gvfs, which will exclude
all files named
.gvfs in the dir-tree.
Instead of manually editing filter rules, you can also run a Compare in the FFS GUI, select the relevant file and use the right-click context menu to automatically add a rule in the right format.
However, given the fact that via your other Exclude Filter entry
*/ you seem to be excluding all sub-directories (and per the
3rd bullet in the Note thereby)
all files in all subdirectories), your .gvfs file must have been in the root of the left and/or right base-location and your
/.gvfs entry should already have been sufficient.
That is, unless, after meanwhile quite some years, there are still some nuances in In- and Exclude Filtering that have escaped me ...