Since changing to the AIR 3.6 I'm getting many errors such as:
Could not resolve <s:Sequence> to a component implementation.
If I switch to the built in Flex SDK 4.6.0 it works fine. I'm using Flash Builder 4.6.
UPDATE
I think that this is because there is a new compiler for ActionScript and that new compiler is included with the SDK and that is causing problems for Flex projects. I read this on the AIR SDK download page (which I did not notice before):
Note : Flex users will need to download the original AIR SDK without the new compiler.
I was using the AIR SDK 3.6 with Compiler. I had to use the AIR SDK 3.6 only (no compiler). There's a link to it further down the page after the text "Note : Flex users will need to download the original AIR SDK without the new compiler."
Are you sure you upgraded to AIR 3.6 correctly? You have to merge it with your current Flex SDK (make sure to make a copy of it first). There are three distinct SDKs in Flash: Flash, Flex, and AIR. To use the AIR SDK, you have to combine it with one of the other two SDKs. You cannot just point your Project Properties to the AIR SDK you get from Adobe. That just won't work.
It's also worth noting that 3.6 is still in the testing phases. 3.5 is the latest stable release and unless you have a specific reason for using 3.6 (you are a tester, namely), you should avoid using it.