Things to check for:

EOS switch on the bottom flipper not making contact (most likely, try pushing it together while activating the flipper button - watch your fingers!)
Blown lower flipper coil (check resistance and compare with the working flipper)
Cabinet switch not making contact (contacts can 'fall out' of the blade)
Bad connector on the SDB - check the schematics and see where the power for the lower flipper comes from

hope this helps!

Thanks for that, I'll work my way through your suggestions tomorrow. I need to get a new multimeter as well, It's not reading correctly.