I get similar behavior. I'm using 3.0.4.1185. It comes back after several minutes, and the track is deleted. Sometimes it helps to work on another app and then come back. Sometimes just coming back seems to make it finish. Have you filed a bug?

Everything was working fine then when I went back later and started up MM I go to find duplicate tracks and i am working on deleting the duplicates. Everytime i click yes to delete from computer and library MM locks up and i have to turn it off and start again. It worked fine at first. I have restarted the computer. if i just delete from library it works fine but that does not do me any good. Please advice thanks