IE has always supported <base href>. By the specifications, it has always been defined only when the href value is an absolute URL, though some browsers have had interpreted it even in the case of a relative URL. It must be placed in the <head> part of the document; otherwise browsers may ignore it. The base address can only be set once in a document. (If this is violated, browsers tend to ignore all but the first of them.)
In this case, my guess is that there is some character, outside any tags, before the <base> tag. Consider this:
<base href="http://domain.net/qu/en/" />
<a href="sample">Sample Link</a>
This is invalid because of the no-break space character before the <base> tag. In HTML parsing, the no-break space, which is not a whitespace character, implicitly closes the <head> element and opens the <body> element. This means that the <base> tag would now be in the <body>. Some browsers may still accept it, but as the document cited in Tieson T’s answer says: “Internet Explorer 7 [and newer] strictly enforces the use of the base tag within the head of the document, and will ignore misplaced tags.”</p>
To check things out, use a validator—it will among other things report problems like this.