The sometimes it works occurred, when I clicked on the compatibility option of IE over 6 times or more. Sometimes I couldn’t ever get it display correctly.
This only started to happen after upgrading to SP5 x64 bit. I used the MSI to do the installs.
Changing the background of the chart to use a gradient made the report work correctly.
To make sure no code was the cause I created a new website which had only one page that contained only a CRReportSource, a CRWebViewer and a NEW Crystal Report, which had a bar chart on it. There was no code written. When the chart had a texture background, it didn't display correctly on the test server. So I replaced the texture with a gradient and then redeployed the site, and it displayed correctly.