Train travel through South Thailand - how worried should I be?

My partner and I are intending to be travelling from Bangkok to Kuala
Lumpur by train in February 2008. We're going to be on a tight enough
schedule that we will not be stopping, apart from changing trains in
Butterworth, between the two; we will be passing through Hat Yai,
though - the only route as far as I know.

The FCO says that all non-critical travel to or through Southern
Thailand should be avoided, but I'm not currently very worried about
travelling (on one train) through the western and of Sangkhla. Should
I be?

Cheers - Adam...