Well, you're not supposed to defeat Ebora -- just her concubines. If you had already entered the Bathhouse before installing the 1.3a patch then the changes would not take effect, however...

There are at least two other problems in the Bathhouse which weren't addressed by the 1.3a patch. Perhaps we could figure out what went wrong in your game if you told me exactly what happened during your fight, but....

You shouldn't have any problems if you 1) fight in RT mode and 2) stay in the room outside of the bath she is in. Please tell me if I don't understand your problem.