This can be solve by changing the background colour in Ubuntu. I’ve tried changing the background colour in Eclipse but it doesn’t seems to works. To change the background colour in Ubuntu, go to
System > Preferences > Appearance
“Appearance Preferences” panel shows up, click on “Customize…”.
“Customize Theme” shows up, go to “Colors” and select a lighter color for “Tooltips” Background, a darker color for “Tooltips” Text.
Start or restart Eclipse, you will see the the lighter colors you selected when the code-assist appears.
This solution is copied from: http://tipstank.com/2010/05/23/solve-eclipse-black-pop-up-code-assist-box-in-ubuntu-10-4-lucid/