Man, I am telling you something strange it is.
I had same problem yesterday.
I had "1.000" in title and "not found" again.

If I clean sh404SEF and joomla cache before I remove that dot, then "not found" again.
If I remove dot "1000" and clean cache everything is working perfectly.

Anyway i know it is not because of sef.

Latest K2 build, latest SVN Joomla.

Maybe it has something to do with my localhost Wamp server and mysql is older version then in my live server.
I tweaked K2 locally and transfered database to server.

It needs some explanation. I can´t explain it.

Maybe sh404SEF K2 plugin is not working 100% perfectly. Do we have a official plugin for sh404SEF??

I have the same 404 problems at www.webfarus.com/kakuxi

SOLVED: I came across a similar bug to this and to be honest, I didn't take the time to go back through all my steps one at a time. On the day it happened I installed a number of Apps and done a cleanup.

It was the cleanup that was causing the strange 404 - Article Not Found in K2

I had deleted an Article called 'Article' from the standard Joomla Articles. When I checked the Article it only had the word Article in it, so I presumed it was redundant. I spent at least 24 hours, reading blogs, researching, uninstalling, reinstalling. Finally I gave up, and thankfully I had backed-up only 2 days before. So using Akeeba Kickstart I reinstalled the whole site.

It was only this morning when I started cleaning up again, I thought, oh hold on one sec. Deleting and checking each group of articles at a time and VOILA. That was it.