To reproduce, do this:
1. open multiple java files in the editor.
2. on Windows XP, using NB 6.9 m1, if you place the mouse pointer on any of the editor tabs and then use the middle button to scroll, the tabs will scroll left or right, so that you can quickly go to the editor tab you want, without using the left and right arrow buttons at the top right of the editor Mode, which is very handy.
3. do a diff between java or xml files (Tools->Diff): a new topcomponent will open in the editor showing the diff.
4. now scroll with the middle mouse button, works fine.
5. now click the tab of another java file and scroll with the middle button, works fine.
6. now click back on the tab with the diff and scroll: it does not scroll.
If you tab out (Ctrl-tab) or click out on another tab and then come back to the diff tab, it will never scroll again.

It only happens in the sequence i described above: if you close the diff topcomponent and open it again, middle-mouse scrolling will work the first time. But once you go to another tab and then click or tab back to your diff, middle-mouse scrolling will never work again.

You can experiment and see what happens with two diff topcomponents and other java editor tabs:the first time you tab between diff tabs, works fine, but once you go to a java tab, and go back to diff tabs, scrolling will not work.

Current workaround: the arrow buttons at the top right of the editor will always work.