Just to follow up on this. I had a similar problem with the syntax of the Apache conf file which prevented it from being parsed resulting in the “Could not choose appropriate plugin: The apache plugin is not working; there may be problems with your existing configuration.” error.
In my case the closing tag had been appended to a commented-out line.
So changing this
# vim: syntax=apache ts=4 sw=4 sts=4 sr noet </IfModule>
to this:
# vim: syntax=apache ts=4 sw=4 sts=4 sr noet
</IfModule>
fixed the problem.