I am having a lot of problems with base href. It is set in the header, before anything starts up, as <BASE href="http://www.mydomain.com/">

The main reason is for pages like
thispage.php?X=123 - I do a redirect to
X/123.htm
which now appears to be in a different folder (mydomain.com/X) - so I need that base href to call other pages, like
mydomain.com/Y.php - I can just put in a link to Y.php, and base href points the visitor to the root folder.

As far as I can see, this is bog standard. But I am getting loads of error messages, I would guess from robots, which are looking for mydomain.com/X/Y.php - they are ignoring the base href.

Does anyone else have this issue?

Pete