A quick Google search turned up several people with the same exact problem. It was kind of interesting. The Ubuntu developers did not want to take responsibility for the problem and said it was an Eclipse issue. The Eclipse community said they never had to do anything special for Eclipse to run on Ubuntu; it was looking like a stand off! I did find the official bug report filed with Launchpad.net, it says the problem is resolved. However, without overriding the following variable, Eclipse is not very usable.
export GDK_NATIVE_WINDOWS=1
It also appears that this problem is affecting many other tools on the new 9.1 release as well. This simple fix will get you back into action, without having to wait for the real fix.