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I have the same problem as some others in other issues already stated : Disqus seems to work fine first, but then nodes start to disappear ( the disqus block is not showing up anymore and the comments are not shown in the "latest comments" blocks anymore )
After a bit of research i'm pretty certain that there is something wrong on the nodeapi hook.
Here is what i what i observed
-> I start with an empty disqus table in the database
-> I have disqus enabled on contenttypes and the comments show up fine on the pages
-> My cron runs and updates some of my nodes with unrelated new data
-> Now all those nodes are in the disqus table with status 0 ( disabled )
-> The disqus comments are not showing on those nodes anymore and when i edit the nodes, the "enable disqus comments" box is unchecked
-> TRUNCATE on the disqus table and everything is back to normal again
I'm not 100% sure where exactly the error lies, but i suspect that either the "unset($node->disqus_status);" on the validate case of the nodeapi hook or something in the update case is wrong and unsetting/ignoring the checkbox.