I've just received a copy of my 2009 tax return from my tax preparer. It's my first year in Switzerland, and I lived a few months in BS, then the rest of the year in BL. My tax has been withheld as quellensteuer in both cantons as appropriate.

I live in Arlesheim, which has one of the lowest tax rates in BL. So I'm confused as to why I find myself owing an extra CHF 4K on my tax return. If I lived in a high-tax area, I could understand how I could underpay on the quellensteuer method, but since I live in a low-tax locale I expected to get some money back (hence the shock at the rather unpleasant news).

The tax advisor has included a spreadsheet showing the breakdown of taxes paid (quellensteuer) and owed in both BS and BL. But I only have a tax return for BL, covering the entire year. Is that right? And if so, do I owe taxes for the entire year at the BL rates, or pro-rated across the BL and BS rates?

I'll call my tax preparer this week to get him to walk me through the calculations, but I wondered if anyone else had found themselves in this position and could offer any insight?