There is some bug in Enigmail v0.95.7 for Thunderbird. If you untick the checkbox “Use gpg-agent for passphrases” in Advanced tab of Advanced settings menu, Thunderbird in anyway will try to use gpg-agent if GPG_AGENT_INFO environment variable is set. The reason is some little bug in Enigmail source code. To fix it, first close Thunderbird, then just open .thunderbird folder in your home directory, search for enigmail.js file. It have to be in extensions folder in one of the random name folders. When you have found the enigmail.js file open it with your favorite text editor and find line number 1368. It have to be this:

useAgent= (this.gpgAgentInfo.envStr.length>0 || this.prefBranch.getBoolPref("useGpgAgent"));

Change the || sign to &&. After change this line have to look like this:

useAgent= (this.gpgAgentInfo.envStr.length>0 && this.prefBranch.getBoolPref("useGpgAgent"));

Save file. Now open Thunderbird and enjoy.