I have checked with the support team, to be sure we were talking about the same problem. The particular issue you are facing is an identified issue in the language switcher module. We already have contacted Joomlart (maker of the T3 template framework) and provided them with the fix. We solely advised you to contact Joomlart to help in speeding up the process of a new fixed release from them.
Yes. sh404SEF may have different behavior from Joomla! SEF or Artio, especially when it comes to multilingual sites. That's because I'm focused on SEO and for instance, sh404SEF will not accept things such as the same URL sometimes returning one language and sometimes another one.
Other extensions may be more tolerant to bugs in some modules, but that comes at the expense of SEO results and that I won't accept.
In other words, your assumption that the problem is coming from sh404SEF because it "worked" with other extensions is not really correct. What happens is that it doesn't work with other extensions either. Simply you don't see the negative consequence now. I have always found that fixing the real, original probem is the way to go.