This all seems to do with adding code to your tests to wait for windows to either appear or disappear before you proceed. You might want to search for topics in the help concerning "Waiting for Objects" and see what you can find.
Something that might be helpful is a screenshot of your keyword test or a copy/paste of your script code so we can help.
As for your naming issues, it has to do with a couple of things. If an object has been mapped to an alias, you'll see it as just the name. If it has not, you may see it as VCLObject.