Splitting up your cardio depends mostly on your schedule. I go to a gym, and I know I can't get there twice a day. So I do a full cardio routine in the morning. Any walking or activity later on in the day is a bonus.
What kind of cardio were you doing twice a day. If you were doing two fairly intense sessions, your body will rebel. If you were doing one intense and one moderate, that's not so difficult on your body.
It could be that you are getting used to the routine and just need a break. Doing something different is the same thing. You are still active, but it's not the same old, same old.
Hope this helps...
Do or don't do; there is no try (Yoda)