After I push a single file and the icon change status to sync the file not updated on the server until I do a full manual sync. I’m thinking its going to wrong location on save and push commands.
When you have the prefs.xml file open you can search for “publishing_configurations”.
Do you suspect that what you have under Tools menu > Publishing > YouAppConfig is not being used correctly by Komodo? Do you have more than one remote server configured for a particular local folder?
Looks like I had the same local uri for two publising locations, When I renamed the config I guess the order reversed (orders by name?) and was sending files using the other location.