Because the tax administration system in France is not efficient. Note that the period in question is the end of '06; your taxes would not have been due for several months after that (I forget the due date in France), and it would take them many months to figure out that you hadn’t paid yet. So, a two year delay is not uncommon… not just for France, for any taxing authority anywhere.
I’m not an expert in French taxes specifically, but I do know that most countries tax income based on residency. You lived in France for more than six months in 2006 (OK, six months and a few days, but that’s still more than six months) and so would need to pay income tax for the entire year as a French resident. The time you spent in Taiwan, you would be taxed in Taiwan as a part-year resident. If there is a tax treaty between France and Taiwan, you would avoid double-tax. If there’s no such treaty, then you’re outta luck.
In short, this could be complicated. Your first best bet is to try to talk to the French taxing authority directly, but I suspect you’ll need to hire a tax attorney who specializes in international situations. (It may be cheaper to pay the damn tax.)