Biztalk Explorer reflects the configuration from the BiztalkMgmtDb database. If changes are made to the config via another mechanism e.g. deploy, import binding file, etc, these changes are not immediately reflected in Biztalk Explorer.
You need to [b:73770f1dd2]Refresh[/b:73770f1dd2] Biztalk Explorer (right click -> refresh) This forces Biztalk Explorer to read the config from the database again
I always check the assembly list and make sure my newly deployed asssembly is there before continuing.