I was having a problem with my sidebar archives links display as
I tracked it back to the function get_month_link in template-functions-links.php
I had to replace the line:
$monthlink = str_replace('%year%', $year, $monthlink);
$monthlink = str_replace('%year%', "/".$year, $monthlink);
and it worked smoothly from there on. I thought this was quite a wierd bug but I'm surprised its not come to light before. There may be another solution to this - but this was the quickest one I saw.