Your partner might have qualified for first time buyer status in 2005. However the property she (& you) purchased was an investment property, and therefore stamp duty is due irrespective whether the purchaser is a first time buyer or not
FTB exemption from SD only applies if the FTB is an owner occupier (i.e. it is her principle private residence).
I have ignored the fact that you, a non-FTB, are a 50% owner of the property as it's an investment property anyway. But there are plenty of threads on similar purchases for a non-investment property. The general consensus is that FTB exemption wouldn't apply in that case either.