Okay, I figured out a workaround. My trick is to rotate everything to Y-up in blender before importing the animation, then Ctrl+A and apply rotation to set the new orientation to 0, then import the animation. After that everything can be rotated back to Z up. Hopefully that helps the OP too.

I am having a similar problem with animation imports. I believe it is caused by the animation having a Y up axis and Blender having a Z up axis. the dmx import Up Axis drop down menu does not appear to be working properly. Importing a model and animation results in the model being correctly upright in edit mode, but pointing up towards the y axis with the animation in object mode.

I tried some older versions of the SMD tools and the same thing happens. Does anyone have a temporary workaround for rotating the animation to the correct up axis without the model facing the wrong way in edit mode?