Ive got a set of pedders lows all round (EL falcon). The problem im having, is that the rear drivers side doesnt stay seated at the top (where the large black rubber ring is. Passenger side is fine. I was wondering if perhaps there is a difference in the heights of the springs due to the weight of the fuel tank, and that the springs are on the wrong sides? Im confident that everything is done up properly, and all parts are where they are meant to be.

How do you mean "doesn't stay seated"? When you jack the car up or after a trip ? Jacking the car up I can understand the spring may drop down, but during driving... well you'd have to be hitting some dips pretty hard IMO...
Nonetheless, I wouldn't think it'd be different springs - but you could take some measurements to see if it is sitting relatively level (measure wheel hub to guard height on both sides). If it seems ok I'd suggest looking at the shock's. Did you get shortened ones installed with the springs or not ? Shortened shocks should reduce the distance the diff can travel from the body and keep the spring seated. Kinda strange though, because I got away with standard shocks in the rear on super lows for a year or so with my old EF (until I got sick of the bouncing)!

It happens when I jack up the car, and from just normal driving around. Makes a huge noise if I do a left hand turn into a driveway. I was thinking it might have somehting to do with the shocks, as they are just standard ones.

If it's only Low's then the shocks shouldn't matter too much, with Superlow's you'd need a shorter shock.

Some manufactureres have a left and right (like King), but it depends on the spring.

Call Pedders and ask them. Surely they would support their products by answering a quick question like that.

Pedders also specify left and right on their springs too.