I just installed version 0.8.8 on my Eclipse (3.5).
If I would like to compare the same class out of different projects then usually I do the following (in Eclipse): on the first file right mouse click, press "store for later compare". Then switch to the other file and press the Beyond Compare button (tool tip: compares the selected resources using Beyond Compare). Beyond Compare opens, but there will be shown only the start screen as if you start Beyond Compare without selecting something. I expected that the comparison of the two files will be shown. This worked in version 0.8.4.
May be this is a bug?