It would be very useful to know the exact command being run by mercurial
here, I don't know if MercurialEclipse has any options to do that, or if
plugins have traces somewhere.

What happen if you enclose the user@domain.com argument in double quotes?

my Mercurial.ini contains:
ssh = "C:\Programs\PuTTY\plink.exe" -ssh -l user@domain.com -agent -v

and hg is invoked in Eclipse v3.5 via the MercurialEclipse v1.5 plugin.
substituting the '@' with something else results in a verbose dialog that
shows the login attempt with the -l string, yet fails as my keys are located
on the remote server based on an ldap account that must be in the form of
user@domain.com (remote policy).

but, with an '@' there is a hang and timeout, no dialog.  the same hg
command issued from a dos shell works fine.  so it's likely not PuTTY.