This is definitely odd. At some point we noticed a particular pop up window appeared during the startup, but for some reason it didn't appear at the front. Instead it was spawned under the splash window. This bug should have been fixed already, though. If this is case, you might be able to simply hit "enter" to okay the dialog if it's there.
Are you using any anti-virus, and does disabling it help?
Did you install NI mate to the default location or somewhere else?