If you try navigate through the same reports in BI Launchpad, do you still have issues or is it just through OpenDocument?
Looking at page 7 of the Product Availability Matrix (PAM) for BI 4.1 SP3, I see that IE 8 and IE 11 are only supported on Windows 7 and IE 10 is supported on both Windows 7 and 8. I also see that JRE 6 is no longer supported as of SP3. So, if any of these conditions apply on the machines where you're trying to open the reports, that's what is causing your problem if BI Launchpad has the same issues as the OpenDocument calls in your application.
-Dell
