Thank god I found this thread. Come on Microsoft, sort it out. I've had a few problems with IE11 and have had to remove it from all our work PCs.
I had been stuck trying to work out why my links were not working for days and didn't realise the update of IE11 had snuck past me!
Same problem, copying and pasting links from email templates and as a small business we send lots out like this each day.
I will remove IE11 as its Windows 7 but I feel for those who may have chose the new Windows 8 for their business needs and have lost the ability to use email templates with links.