In the current Beta, if the schemas are filtered the schema dropdown in the commander window shows a different set of schemas - not the ones filtered in the tree.
I cannot reproduce this with the latest Beta (95.2536). One issue with regards to filtering schemas that we are aware of is that the lists in the SQL Commander are not updated until you make a reconnect after enabling the filter. Could that explain what you see? If not, please include screenshots to illustrate the problem.