Hi Malik,
It might look like an issue but its happening due to Java and HTML interface architecture in XI 3.1. When you open the report in Edit mode, visual effects are handled by Java so alignment are proper. But when report is opened in View mode, its handled by HTML, so alignments are poorly handled.
That's why BI 4.0, Java has taken over full BI LaunchPad application. And even viewing a report is handled using Java so you don't feel the difference. So if you need proper alignment in view mode then you might need to upgrade to BI 4.0.
Are you facing alignment issue if you export report to PDF from View mode? If yes then please confirm. We can fix that issue.