IE Window Won't Allow Input

We're running an Oracle application that requires the jinitiator 1.3.1.22 on the client pc. Prior to Windows7 we only had a problem that required replacing the jvm.dll file within the Jinitiator installation folder. With Windows7 64bit and/or 32bit, we're seeing where some clients can open IE9 and get the popup logon screen as expected but nothing you type will show in the logon area until you click outside of the window and then come back to it. We've noticed that unless the cursor is blinking in the logon window it will not display anything that is typed (unless you click outside the window and come back to it). However, some users can use the 32bit IE and never have a problem. Sometimes you'll get a message that Windows is changing the basic theme.