Link checker does not seem to see some broken links-why?

Hi,
I have a problem with the link checker, it does not seem to report some broken links. Here is the context in which it happens.
My site root folder contains (subset) :
index.php
Templates/child_userarea.dwt
user-area/downloads.html
(The file downloads.html is based on child_userarea.dwt.)
In the template, I have <a href="../../index.php" title="Home page">Home</a>.
In downloads.html, this link appears as <a href="file:///M|/Website/index.php" title="Home page">Home</a>.
According to this post http://forums.adobe.com/message/934203#934203 by Murray, this is because Dreamweaver (CS4 in my case) thinks that index.php is outside the site root folder. I understand it thinks so because indeed ../../index.php points to the folder parent of the root folder. What I don't get is why doesn't the link checker report that ../../index.php does not exist? (And I'm sure it doesn't, there is no file called index.php outside the root folder.)
Emilie

That's the thing, it is correct! I have checked many times. Here is what is says:
and M:\Website\CERC15\ does exist.
For the time being, I have corrected the paths in the template, so for that particular file, it is now ok. However, I have no idea whether other paths are wrong since I am not sure any longer whether they are spotted by the link checker. I searched for other instances of file:///M|/Website and there is none left.
I suspect this is just one more problem due to another problem non-identified so far (see e.g.http://forums.adobe.com/thread/506149?tstart=30). Since I renamed a big batch of files, I have had problems after problems: the templates disappearing (see that other post); I also lost all the files in 4 other folders (files for download linked to the pages through <a> tags); and Dreamweaver has become particularly slow (but this seems to have been fixed with erasing the cache and the personal preferences).
I'd like to start from scratch again (and why not reinstall Dreamweaver), but I don't know how to recreate the site from zero without loosing anything (e.g. links to templates).

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    Message Edited by toomanydonuts on 04-22-200705:50 AM
    Message Edited by toomanydonuts on 04-22-200706:10 AM
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