Ok so I think I may have solved my issue which maybe a silly error on my behalf or something has still changed in later versions of retropie because I don't think I've ever had to change controller types.
But even though I've solved one problem it appears to have created an new problem.
Firstly I'll start with saying with default settings I usually have just turned on game specific options, started game, enabled multitap 1 in retroarch and all has worked. But it hasn't this time that's why I've had problems.
But what I have just done is changed player 1-4 controller type from default to standard and micro machines v3 has just worked with all 4 controllers.
I've then launched hogs of war and that has worked making sure controller type is analog.

So firstly i would like to know why player 1 and 2 controller would work with them all being on default but controllers 3 and 4 wouldn't.

Now onto my new problem.
When setting multitap and controller type in options and saving game specific options, a yellow notification pops up saying core options saved.
And it appears to be saving it across all games as a core option rather the game specific option.
I have double checked and game specific options are set to true.

Thank you all for your help I'm almost there :)