I too have the issue that windows reverts to 5.1 when using headphone port. I don't think that it will do hurt anything if you do not use the SBX stuff though. In stereo mode it doesn't revert to 5.1. By the way, for headphone mode this might be working workaround:
and then select full range speakers form the next page. I haven't tested but I think those settings won't revert.
Edited by Anarion - 6/7/13 at 11:26am