as for your first question , provide a link to your install so I can check what the module holder z-index is set at , seems like template is overriding it and I would say T3 mega menu does it
Hi there and thanks for the follow up. I am now back from the holiday season and catching up on a few things.
Unfortunately I can't provide link as it is in a local install with wamp.
However I have scoured my css and as you guessed it was the mega menu z-index causing the overlap issue. Set it to a lower setting gradually until it was resolved. I haven't noticed any side effects from it so it seems to be working now for the overlapping issue.
As for the SEF issue I thank you for the info. I have tried it with a few other login modules and I get the same results. This tells me it is not your plugin, but something else in the joomla settings/code. I will let you know what I find if anything. Thanks