Had a similar issue last year with my employer. Working with them a number of years, new system implemented and a few of us were effected. After 2 months (pay packets) being incorrect enough was enough. Went to Finance dept and insisted a cheque be written their and then for the amount outstaning plur referral fees for payments being missed from my account. Usual story of can't be done etc so got brazen and knocked on door of Dept Director. Expalined issue, he said it will be sorted and lo behold at midnight two nights later all monies paid to my account.
You need to suck it up and demand money for the work you've done. Money being left short in your wages doesn't affect the wages dept, it affects you and they should be made accountable.
By the way, I still work the same large company, there was never any backlash.