Pension payments made in 2006 will not be covered by your 2007 tax credits as far as I know and you need to claim the tax and (separately) PRSI back manually by writing to Revenue with the relevant details (e.g. copy of PRSA1 certificate and P60 any any other relevant info). They should then do a balancing statement for 2006 and issue any outstanding tax relief. PRSI is handled separately - see the key topics in this forum.
As for your 2007 tax credits can you post precisely what it says about pension/retirement annuity credits and also about your standard rate band and to which period (e.g. year, month or week) that the figures apply.