Can you try opening project properties > Flex Server and then check if your
project settings validate?
I did get the problem that originally got me to post to go away but there's another problem.
I don't know how many others are experiencing this issue but when checking the properties of the server they never stay the same. Every time I fix it from J2EE to standalone CF it says it applies that I save, but upon return the settings have reverted.
I have uninstalled and reinstalled and to no avail. Just seems to be a very strange issue
In order to correct the original issue I uninstalled then cleaned my registry, rebooted, and reinstall. That seemed to get it working however those server settings continue to revert any time I open the menu.