I'm running Debian Jessie and I seem to have the problem as well.

First, I have two main Firefox profiles, "default" and "empty".  Empty
has few extensions while default is my fully loaded profile.  In order
to be able to easily run them, I create custom .desktop files that
execute "firefox -P <default|empty> -new-instance %U"  If I don't use
the "-new-instance" (or "-no-remote"), and I decided I want to run the
empty profile but the default is already running or vice versa, I get
the "already running error".

It seems, when I create a shell script to execute "xterm" and set it as
the mail application in Firefox, I get a bunch of MOZ_ environment
variables.  I played around with un-setting the variables before running
Thunderbird.  It just so happens that, at least for me, if I unset a
variable "MOZ_NEW_INSTANCE" then it seems to work.  To verify I start
Thunderbird and then open a terminal without any MOZ_VARIABLES and
execute "thunderbird mailto:[email protected]";.  Everything works.  If I
then execute "MOZ_NEW_INSTANCE=1 thunderbird mailto:[email protected]"; I get
the "already running" error.

So it seems that what is happening, at least for me, is when I run
Firefox with -new-instance, it sets an environment variable that is in
turn passed to child processes.  When I click on an email link it
launches Thunderbird, but that environment variable is set and
Thunderbird tries to start a new instance.  The same seems to happen if
I use -no-remote instead, it just sets a variable MOZ_NO_REMOTE=1

I create the following script and set it as the mail handler for the
time being.

    #!/bin/sh
    env -u MOZ_NEW_INSTANCE -u MOZ_NO_REMOTE thunderbird "$@"

Currently there is no way around "-no-remote" or "-new-instance" with
Firefox it seems.  If I launch one profile, and wish to launch another
profile, then it will complain unless I use one or the other.  Ideally,
there should be a way to launch multiple profiles, but to have "remote"
features with both, either designating one as the default to receive
remote commands or a chooser to list available instances to receive
remote commands.  For now, the shell script to remove the environment
variables seems to help.

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https://bugs.launchpad.net/bugs/711305

Title:
  Thunderbird is already running, but is not responding. To open a new
  window, you must first close the existing Thunderbird process, or
  restart your system. Error received when clicking a mailto link in
  firefox.

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