lammert - 3:23 am on Oct 9, 2010 (gmt 0)
You can add the /path1/path2/ URL part and it shouldn't confuse Googlebot, as long as the internal URLs are all absolute. What I expect to be happening based on my personal experience is that not Googlebot is off-track, but a bad bot throwing out a Googlebot UserAgent string. In the logfiles it looks like Googlebot makes an error, but you have to check the IP address to be sure it is really a visit from Google and not a wolf in sheep's clothing.
Another thing which should be considered is that this /seo_page.html doesn't show up for some other obvious reason, like excluded in robots.txt, over optimization etc. Because even if on some pages the link to the page is corrupted based to a wrong base href tag, it normally should have been found based on the following statement of the OP:
Even though there were 10 correctly coded links throughout the site for every 1 that had an incorrect path (based on the <base> tag) that Google saw, Google never reported the correct path/pages.