We do test with sh404SEF in some ways, but just not for every automated test. We actually use sh404SEF on this site, so we try to ensure compatibility.. however, it's impossible to run our full gamut of tests with every possible Joomla configuration setting and all 3rd party extension, but we try to run quite a few common configurations. Then, of course, when an issue is encountered, we do what we can to fix them as quickly as possible, as you know
Thanks again for the report, and glad we got you fixed up!
Alex