STB has nothing to do with audio coming from files being played from USB hard disk. So whether STB is connected or not makes no difference.
ARC essentially means that whatever audio output you are getting from TV speakers, that audio will be sent to HT-S3400 and it will be output through HT-S3400's speakers.
So say you connected 10 devices to the TV (some via USB, some directly via HDMI, etc, etc), then you select one device and you start playing something from it on TV. If you are getting audio through TV speakers, you can send it to 3400 via ARC.
But you need to turn ON ARC in HT-S3400 for this to happen. The way to do this is...under HDMI Setup --> Audio Return Ch (ARC) set this to "Auto". Then when you want ARC to work, which means output audio from TV speakers to HT-S3400, you select "TV/CD" under "Input Selector" from HT-S3400's remote. Some people think just by connecting devices to ARC ports via HDMI cable will make ARC work, or you need special HDMI cables for that.
Now in your case, you must have set Audio Return Ch (ARC) to "Auto" and you have selected "TV/CD" from remote (or previously had selected "TV/CD" before switching off HT-S3400, which means when HT-S3400 is switched ON the next time, it will start in "TV/CD" mode automatically). So when you switch ON HT-S3400 and play something from hard disk audio is output through HT-S3400. So now you know how to turn this OFF when this happens.......select anything else other than TV/CD from remote.
This is not an issue. It's a feature, if you may.