You selected another .xml file other than your keystore file (Check the Credentials box – it should show the name of the holder of this keystore file;)
Your keystore file is corrupt;
I'm a BAS Agent and 12 months ago I decided that it would be quicker using GovConnect too. I had the same errors back then even though I could login through the BAS Agent portal (to ATO) using the same credentials. I discussed this with both Reckon and the government department that looks after Auskeys (can't remember their name, off hand). Both wanted to blame each other for the problem. In the end I just continued using the Agent Portal. Sorry it's no help to you but atleast you know the problem isn't yours alone or it being a one off problem, it has been happening for more than 12 months and it would appear that no-one is going to put their hand up and say "I can fix it".
As far as files being corrupt, I use the same credentials at least 12 times a month and have never had credential problems when accessing the portal.
PS I un-installed GovConnect about 2 weeks ago!!!
Regards Andrew