Oh ok I roughly know why now.
Basically it's something to do with surrond sound support of the SupCom engine. I hope they fix it, but chance is probably slim.
I am using 5.1 srround downmixed to headphone by my speaker. This has no problems in other games. Usually it's acceptable in SupCom too. But I guess it'd mess up sometimes. The root cause is bad 5.1 surround sound support in SupCom engine. Channels audio would all be swapped. Front sound would come from back speaker, and vice versa.
I am using Auzentech Prelude soundcard, a re-brandeed Creative X-Fi.