Odd, I use them there in a few projects and it works fine.
Make sure you are adding them to a Build Configuration that is currently active in your project. Not sure what your project setup is like but IntelliJ will only use the settings from the active build configuration you currently have set.
Another alternative to using the "Conditional Compiler Definitions" table, is to use the more cross-tool flex-config xml configuration file format.
Ie, defining XML files like:
<?xml version="1.0" encoding="UTF-8"?>
<!--
Additional compiler configuration options passed to the compiler
Abstracted even from within IntelliJ so that it is easier to manage
and see custom settings within an easier editable file
NOTE: This file is a supplement to default configs and
settings in the configuration file take precedence over the ones specified
in the IntelliJ UI table.
-->
<flex-config>
<compiler>
<define append="true">
<name>CONFIG::air</name>
<value>false</value>
</define>
</compiler>
<!-- Equals SDK version + 11 using the newer SDK numbering system -->
<swf-version>29</swf-version>
</flex-config>
Then you can just reference the XML file path in the field "Additional compiler configuration file: "
This not only lets you avoid using the custom GUI in IntelliJ but also allows this same build-config file to be used with command-line builds used as the compc -load-config value.