Is your htaccess setup correctly? Bare in mind if you've downloaded it and placed it into a subfolder you'll need to ensure the htaccess is modified to account for the folder.
What is being posted out in the source code when you have
<base href="[[!++site_url]]">
And what is being posted out when you inspect an anchor link to another page?
It's been working fine for several weeks now. The only thing I can think of is that yesterday, I removed all deleted resources. But you're right, I looked right past this. The posted url is appending an "en/" to the end of the url. No idea why though.
Do you have a multi context site setup? In your context setting do you have the en/ appended ?