did you move back into property "a" in 2005?. i'd look very carefully at the timing as, because as i understand it, you can claim a property as your ppor for 6 years after you physically vacated the property - you can't just pick a date to start calling it your ppor from.
even if you moved back in for 2 weeks and had the electricity connected in your name for that period, that qualifies to reset the 6 year claim period - so you can claim the cgt free period indefinately - as long as you move back in each time "before" the period is up.
personally, if you didn't move back into the property in 2005, i would have thought that the 6 year ppor period would have started in 2003 even if you were calling your property "b" your ppor during that time.
you may want to get some expert accountant/ato advice on this.