"Move to junk" just makes a copy of the email in the junk folder but keeps a copy in inbox.

I am clicking “move to junk” for some emails but it doesn’t move the item out of my inbox, it just makes a copy of it and puts the copy in the junk folder, while still keeping a copy in my inbox.  Is this how this is supposed to work?  

No, it is not supposed to work like that. There may be some corruption with the message cache, or some issue with the server.

Who is your email provider, and is your account setup as POP3, IMAP or Exchange?

It may also make a difference if you have checked the email on your phone as well but then that goes back to is it a POP3 or IMAP setup?

Thanks!  No its all done on the computer … We use google apps email … it is setup imap … I dont know why but it’s only doing this on one computer and not others.

You could remove the email account from eM Client on that computer, and then add it again. See if there is any difference.