Well the calculator is assuming you're a first time buyer this year. The rate for 2012 FTB is 25%. As you know, a FTB in 2007 would be entitled to 30% (from 2012 to 2017).
There is a ceiling on the amount of interest on which you can obtain relief; €10k for a single FTB (€20k for a married couple).
So the calculator is calculating maximum relief for you, at 25% of €10k = €2,500.
Now, as for the difference between the interest you've calculated and what the calculator calculates:
When you start paying a mortgage, every payment includes an amount of interest and an amount of the capital (unless you're paying interest only), that's how the loan balance reduces. So every month the amount of the loan balance is falling slightly, and accordingly so is the amount of interest, as it is being charged on a slightly lesser amount.
In your case then, since you would be paying interest in excess of the 10k limit for at least the first few years, you should be getting €3,000 of mortgage interest relief.