Today I was forwarded with Google's Webmaster tool alert message saying that the Googlebot couldn't access the site
This part, by itself, can be ignored. It's a long-standing known issue. You can test it for yourself using Fetch As Googlebot.
I don't see the part where you tried and failed to add the without version to your own account. You have to put in both versions explicitly, even though g assumes it is the same domain. Yes, you yourself have to maintain Duplicate Content in wmt ;) Some areas, notably Links To Your Site, carry separate information for the two forms of the name.