Hi ,
I installed blender 2.73 and did see what you are talking about with the bone rotation going wrong, however I believe it may be a bug in blender’s export system. When we exported to an FBX and opened the FBX in Maya with X Forward and Z Up, the bones seem to be facing the -X Forward instead of the X Forward. After adjusting the the -X Forward and exporting to the engine, I still received a bone rotation warning but all of the bones seemed to come in as expected. If you could, try exporting with -X Forward, and Z Up and see if the .fbx imports as expected (character facing backwards with bones correctly aligned to mesh).