In the Kobo eReader.conf file (found in /.kobo/Kobo in the USB exposed connection), you will need to find a header named [FeatureSettings]. If you don't see that heading, you will need to add it. Under [FeatureSettings], you will then need to add the ExcludeSyncFolders=\\.(?!kobo|adobe).*? line.
What you should see after that is a section somewhat similar to:
Code:
[FeatureSettings]
ExcludeSyncFolders=\\.(?!kobo|adobe).*?
IgnoreCaptivePortal=true
InvertScreen=false
Screenshots=false
Please disregard the extra lines.