It is because of the different bone orientations. You'll just need to adjust the localPosition/Rotation of the IK targets that should be parented to the HMD and hand controllers.
The easiest way to set up a new character is this:
1. Add VRIK
2. Move the HMD and hand controllers to the model, as if they were worn by the model.
3. Duplicate the head and hand bones
4. Parent the duplicates to the HMD and hand controllers
5. Assign the duplicates as head and hand targets in VRIK.
Tutorial for SteamVR here.