Valve's SDK updates this week (which appear to be ongoing, so this could all change) have introduced a brand new set of SDK tools for TF2 and Portal mapping. Sadly these tools do not work with games based on earlier versions of the source game engine (such as EX and every other mod).
It appears they have also move the SDK tools that do work with mods to another location, along with their copy of the GameConfig.txt
At the time of writing the GameConfig.txt to configure for use with EX can be found at $steamUserDir/sourcesdk/bin/ep1/bin/GameConfig.txt
To run the EX compatible set of the SDK tools that use that config you have to go into the tools tab in steam, right click on the Source SDK listing and click on Properties in the popup menu. In the properties window on the General tab is a button labelled "Set launch options...", which pops up yet another window with a single text box in it (it says it's for "advanced" users only, but you need to use it to map for any source game except TF2 and portal...). Type the following into the box
OK, from now on when you run the SDK it
should launch the version compatible with EX. If you want to map to TF2 or Portal you'll have to take that option out again. I get the impression valve are actively making updates to the SDK at the moment, so this could all change without warning.