currently my cc2017 version is saving all mixdown files as Wide orbit wavs. unlike cs6 and 3.0, theres no way to adjust the default.
add the same feature you had going back to 3.0. it was under edit/preferences/system tab
"default format for save as dialogs"
The default format when performing a "Save As" will always be the same as the original file. If you use File > Export to save new copies, it will always remember the last-used setting for this dialog.
In this case, it sounds like the WO importer is being used to open these files. Are they tagged with WO metadata? If not, then when you open the wav files, make sure the "Enable" dropdown in the Open Files dialog is set to "Wave PCM" and not "Wide Orbit"