So, usually IMF is a slideshow for me, and I've come to accept that this will never be fixed. However, the boss fight level is always smooth as butter for me, and today was no exception (post patch).
That is, until I finally killed one of the twins and the giant token came down. Suddenly instead of 50-60fps I was getting 5-6fps, and it persisted until I got to emberlight. Either this is a very rare, random bug, or (much more likely) a serious regression in the latest patch.
Or maybe it's SK's way of getting back at me for killing the twins with a needle shot? Hard to say...
Were you playing with your graphics on high?
Also, are you using the standalone desktop client or the Steam client or what? The only thing I can think of that would do this is the patch, like you mentioned, a change to Java or something else running on your computer that's slowing you down.
If you ever figure it out, let us know please. I have that issue with IMF too, but playing with the graphics on low helps a little.