Atahualpa provides two links for older comments. The one on the top works well, the more useful one at the bottom of the page (if sorting newer comments on top) is not working but linking wrongly. If I deactivate Atahualpa it is working again.

See example here: http://openmtbmap.org/download/
On top link is correct to: http://openmtbmap.org/download/comme...e-18/#comments
On the bottom link is broken and goes to: http://openmtbmap.org/comment-page-18/#comments

If I switch back to 3.4.2 it is working alllright. It is broken in 3.4.6

(actually I'm really getting fed up with Atahualpa 3.4.3 and above. 3.4.2 was the last version that worked out of the box more or less. Since then it's patching bugs bugs and bugs. 3.4.3 was the last real update anyhow since then it more or less seems that Atahualpa is not developped anymore. Since more than 8 month, there has been no real work done on Atahualpa, nor bugs removed like the crazy Atahualpa Page Options that cause havoc if not switched of and much more. Even little bugs for which fixes were posted on the forum, got carried forward to updates, simple things like putting images in a relative folder still not default causing loads of work on each update,..... I'm seriously considering switching the theme for Wordpress 3 as Atahualpa is causing too much trouble and it does not seem like there is any work done keep Atahualpa one of the best plugins like it was before, or maybe offering Atahualpa as SVN so one can easily carry forward fixes from version to version...).

What's your permalink structure set to?
the issue is the top link is showing the full path, but the bottom link is dropping the 'download' in the address.

have you tried with all plugins disabled?

Permalink structure is /%category%/%postname%/

I have tried with all plugins disabled. Still broken. It is definitely a bug in Atahualpa 3.4.3+ as it is still working if I downgrade to Atahualpa 3.4.2 but broken in 3.4.4 or 3.4.6.

Actually I discovered that in the comments section here someone else if having the same problem: http://forum.bytesforall.com/showthread.php?t=6568

The only major modification to Atahualpa I have done is disabling the Atahualpa Page Options, as they are incompatible with qtranslate and many many other plugins.

This is defnitely not a permalink issue, but an Atahualpa bug (no problem using other themes, no problem on 3.4.2) - maybe related to disabling the page options that seems to cause some problems.

The cleanest solution would probably be to backport changes from 3.4.4 to 3.4.6 as since 3.4.3 Atahualpa has become unstable and buggy.

While I can see that there is a problem on your site, I can not recreate it on a vanilla install of 3.4.6, which leads me to think that something else is happening. It may well be related to the removal of the ato post otions and or qtranslate.

Do you remember the post that showed you how to remove the ato post options?

Yes, it was this post here: http://forum.bytesforall.com/showpos...17&postcount=3

However of course I now only remove the section itself, unlike at the time of writing to the end of the document...

I have attached my functions.php (based on 3.4.6) on this post.

I just noticed this is a PAGE not a POST - I've been looking at POST comments. Let me check out PAGE comments