This can be replicated in Windows running Apache.
I exported the XML file from regular wordpress and tried to import to Wordpress MU with the "Download and import file attachments" checked.
The posts imported successfully, however all the JPGs were not imported, and I got the error "Remote file is incorrect size" for every file.
I traced it to /wp-admin/import/wordpress.php (line 587), and found that:
filesize($upload['file']) is ALWAYS ZERO ??!!!
$headers['content-length'] is correct size
$upload['file'] has C:\webroot\www.mysite.com\blog/wp-content/blogs.dir/2/files//2008/01/DSC01023.jpg
As you can see, there is "//" in the path, and it is mixed with forward and backward slashes.
That was the reason why it failed, however, when I monitored the file folder during the import, I saw the files were actually written to the file system, and then got deleted ("unlink" the file)
To fix this:
/wp-admin/import/wordpress.php (line 582) insert these:
$upload['file'] = str_replace("//", "/", $upload['file']);
$upload['file'] = str_replace("/", "\\", $upload['file']);
and problem is fixed.