I didn't realise that was the way it worked. I've been using a makefile from ::[ edam ]:: » Arduino Makefile to build my sketches, so I hadn't noticed that .pde isn't recognised by the new IDE (if that's the case). (Before I switched to this makefile, I was using the one that came with earlier releases of arduino).
I switched to arduino 1.0.1 (from the earlier version that came with ubuntu) because I was wondering if there was a bug in NewSoftSerial that had been fixed in the latest release.