If follow doesn't work either, I'd suggest checking to see if the addon is enabled on both characters.
IS Boxer uses its' addon to generate the macros (including FTL Assist and Follow).

If that is not the case.
I believe 'F11' and Backslash '\' are they keys which are sent to the windows.
With your FTL modifiers added, to initiate follow & assist.
Check that you don't have any conflicting keybinds on the window that is not following.
Basically open your keybinds and pick a blank one... then bind Shift F11, Ctrl F11, Alt F11, Shift + Ctrl F11... going through each combination of F11 and Backslash.
Unbind/Clear the keybind as you make them, so you're sure that key bind is free.