Issues with security warning popups in JRE1.5.0_06

Question

Using
Java Plug-in 1.5.0_06
Using JRE version 1.5.0_06 Java HotSpot(TM) Client VM
Browser is Internet Explorer 6.0.2800.1106
Background:
Our web application has 3 different applets on one page, transmitted using https. Due to a variety of factors, the name of the host does not match the name on the certificate, and we can not change that.
Problem:
We get 3 dialog boxes warning us that the names do not match, as usual. However after installing 1.5.0_06 we get 2 different undesirable behaviors:
A ) 1 or 2 of the dialog boxes are empty and small, as if only the window of the dialog box was created, with no components on it. When you resize them, they remain blank (only default background color). They can not be closed.
B) All 3 of the dialog boxes look as they should, but only one of them can be interacted with. Even after we press "Run" on the working dialog box, we are not able to interact with the other two dialog boxes.
The applets causing these security popups are in 2 different frames, and load simultaneously. The popups all appear at the same time .
We consistently see different behaviors on different PCs:
PC I : After 30 tries, it fails once, error B
PC II: After 20 tries, it works once, mostly error A
PC III: 10 tries, Mostly error A. Never worked once. After a reboot (and full cache clears) we get mostly error B. Never works.
If we disable the warnings (in the control panel), the page loads ok, with no errors.
Have anyone experienced this ?

Answer 1

I've experienced similar problem with Java Web Start twice.
Also using JRE version 1.5.0_06 Java HotSpot(TM) Client VM and Browser Internet Explorer 6.0.2800.1106 on Windows XP (Problem was the same with Java 1.4.2)
My application was signed and launched via JNLP. The security warning popup was shown in the windows taskbar, but it was hidden. Using maximize in the taskmanager, I was able to see the dialog but it was blank. The problem was persistent, although I did not try as many times as 20-30 :-)
On both occations the problem occured on multi (3) screen systems, which I suspected to be the problem (Java has historically had some issues regarding multi screen systems), but now I'm not so sure.
Did you find a solution / cause?