Tax Refund turned to Tax Due

This is the first time I have experienced this with a company, Our old company was bought out by another and it has been three months now with the new company and that's when we got news about our tax refunds. Apparently our old company was paying taxes annually (our new company pays monthly) and they got bought out October of last year (official transfer of rights to the new company). Our finance people explained that our old company did not pay our taxes for the next payouts so we paid for it. Now our new company had us paying our taxes for them as well.. so we paid DOUBLE the taxes for the past months?

I'm confused at all this tax paying stuff.. I hate the feeling of being ripped off.. anyone with any answers about this issue? And how can it be possible that we have to pay extra (which would be deducted automatically in our salary months and months to come). How come we did not get any refund from our previous company?

I found an online calculator that calculates tax refunds here http://www.wraithstrider.com/witholding_Site/pages/salary_index.html. No matter how I calculate.. I am sure that I should be getting something back.

is this in the philippines? get a certificate of tax withheld by both companies. compute your tax based on your actual income, then just declare an overpayment and use it as credit for your new taxes.