The "target" attribute is forbidden in XHTL 1.0 strict. Moodle doesn't validate with "docs in new window" on.
A possible workaround might be to use JS:
<a onclick="window.open(this.href); return false;" onkeypress="window.open(this.href); return false;" href="abc">text</a>
If the browser does not support JavaScript or it's no enabled, the link will open in current window.
Found http://lists.evolt.org/archive/Week-of-Mon-20041018/165515.html