SuSE 10 - Recording sound only on one speaker?

Hi, I've just installed SuSE 10.0 and I've spotted a real funny one. I'm using Line-IN to record stereo sound, and when I allow sound to play directly from Line-IN, it comes through ok. However, if I use an application to capture the sound, then I only get the left or right portion of the sound! Please note, my machine is multi-boot, and I'm using the same software and version numbers (Myth-TV), under 9.3, and all works fine. I've checked alsa-mixer (and kmix), both are set at same recording levels on both stereo channels... I'm puzzled - I've never seen this before.... Has anyone any ideas? Thanks Carl