I don’t think that I’ve ever seen defined benefit plan that required employee contributions. Are they voluntary? Also, I agree that it’s odd that the contributions were taken out of pre-tax money and required that you ‘settle up’ taxes on the back-end (or did you adjust your w-4 withholding to give yourself ‘credit’ for the pension contributions?)
One note — you can generally make contributions to your IRA until mid-April and still have it apply on the prior year return. If you withhold your contributions until you get your taxes figured out otherwise this can help to give you some flexibility. It’s also prudent since as you’ve found, once you contribute money to a retirement fund it’s pretty much locked there unless you’re willing to part with an early withdrawal penalty.