New windows covered by top panel
Solution 1:
Answer approved by OP in comments.
Have you tried
CompizConfigSettingsManager-> Windows Management-> Place Windows? I have this happening in 11.04 with a third Writer document window opening above the first Writer document window and hence, under the top panel. This did not happen (to me) in 11.10 which I have been using since beta 2 so I never tried finding a permenant fix.