The game does not see Joystick Gremlin inputs, only the original joystick ones.
This wil happen quite often as Joystick Gremlin cannot hide the physical devices inputs. To circumvent this issue the Input Repeater tool was implemented. You can activate it via Tools > Input Repeater. Once activated go into the game's input remaping screen, use the input you want to map by either pressing or moving it. Then, activate the remapping dialog of the game and it should recognize the virtual joystick's input. The input repeater will repeat your input for a duration of five seconds.
An alternative to this is to effectively hide the physical devices from the application such that only the virtual devices are seen. Software like T.A.R.G.E.T is capable of doing this already. By using HidGuardian any HID device such a joystick can be hidden from all non white-listed applications. Joystick Gremlin can configure which devices should be hidden by HidGuardian in the Options dialog.
How to verify that Joystick Gremlin produces the desired output?
The simplest way which doesn't require any additional tools is to use the Windows game controller program, which can be launched by running joy.cpl. To see the output simply open the dialog for the desired vJoy device. One drawback of this tool is that it requires focus to show anything which can be a bit cumbersome at times. Some alternative programs which can show information about various joystick devices are:
Macros don't work in-game
The most likely cause for this is that the game was launched with administrator privileges while Joystick Gremlin was launched with normal user privileges. As the macro system injects key presses into the Windows event system Joystick Gremlin has to have the same or higher privilege level as the receiving application. As such if the game is run as administrator then Joystick Gremlin needs to be run as administrator as well.