Thanks guys!
I fiddled with some of the settings suggested by Mr.Wizard, none of which solved the problem, but then after switching back to LilyPad and reentering the inputs, I noticed on the list in the left panel that sometimes entering an input for one direction on an analog stick (this happened with left and right) would overwrite the previous input entered.
So, for example, after clicking 'Left Analog Stick: Right' and moving the stick to the right, it would show up on the list as 'DX USB Joystick, X Axis +, L-Stick Right', then clicking on 'Left Analog Stick: Up' and moving it up, that list entry would be completely replaced with 'DX USB Joystick, Y Axis -, L-Stick Up'. Both correctly entered for what they were supposed to do, but one replaced the other :/
Anyway, problem solved after chasing directions around for a while (as they occasionally replaced each other) until they were all there, dunno if it's a bug with LilyPad or pcsx2 or some quirky fault in the controller, but at least it's fixed
Apologies if my reply is overly wordy, I wanted to clearly spell out the problem and my workaround in case anyone else encounters similar and goes looking for solutions. Thanks again for the quick replies, guys, sorry it took me a while to respond.