I ran into a very interesting issue last week involving a CRM 4.0 organization that was upgraded to CRM 2011.

The organization had two custom security roles in use and for some reason, those security roles didn't have any security applied to Web Resources ( shown below ):

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This issue surfaced in a very odd way: Users with these security roles were not running the JavaScript that was applied to the form, so that none of the form modification code was being executed and/or random script errors would appear.

I am not 100% positive how this situation occurred, but adding Read access to Web Resource seemed to fix the issues.

So, if you are upgrading to CRM 2011 and have custom security roles, verify that Read access for Web Resources has been applied to those roles.