Thanks for your report, but I can't reproduce the problem (using Tunnelblick 3.4beta16).
My config file has
ca "myca.crt"
and a file named myca.crt is in the same folder as the config file (both are in the folder /Users/MY_NAME/Application Support/Tunnelblick/Configuration/FOO).
If the config file is in the ...Tunnelblick/Configurations folder, and the myca.crt is in Tunnelblick/Configurations/KEYS subfolder, for example, you should have
ca "KEYS/myca.crt"
in the configuration file.
What version of Tunnelblick are you using? Can you describe the path to the configuration file?