This doesn't happen all the time - which is why I think it is a bug rather than something I am doing wrong or differently sometimes.
Why I run HM Sync sometimes I am told I need to enter my password in the settings window. When I try and do this I am told I didn't login to my HEM account, so I then have to enter my email address and password into another pop-up before I can save my password in the settings window.
I synch between two PCs fairly frequently and this seems to happen about 1 in 5 times.