I suffered from the very same problem, but I just found a solution. Hope it works for you, too:
go to the command line and run
smbclient -L server
when asked for a password, just hit enter, as the guest account should be sufficient for listing the shares and some info about the server. Look for the Domain=[domainname] output.
If you know the domain of your samba server you can of course skip the smbclient call.
Now try to log in but replace the MYGROUP in the domain field of the pop up with the correct domain of your server. Using the proper domain worked for me and I could access the shares again.
I think it is quite a regression that Fedora 15 could figure out the correct domain to use and you have to provide it manually in Fedora 16...
But I guess it is not a gnome problem, but somehow related to changes in samba.
In Fedora 15 I could browse shares using
smbclient -U username //server/share
now I have to use
smbclient -U domainname/username //server/share
otherwise the call will fail with