I'd go back to the TMO you had previously for now. But I will point you at
MultiSH4 for future reference. The download link on that page isn't any good, but it is here on subsim at:
http://www.subsim.com/radioroom/down...o=file&id=1110
That little jewel of an applet will allow you to change the Save folder of a 2nd install of SH4, if you can manage to do that with Steam (I haven't tried it yet myself). If you can, you could have the TMO install and a FotRSU install that you could experiment with, each with a Save folder that you named... I'll see if we can find anyone who has done a Steam install since they did that update about a year ago... I'm thinking it can be done by changing the name of the install folder, but I'm not certain...