Java SE (Java Platform, Standard Edition)

I have an applet embedded in a html page (using the object tag) referring to JRE 1.6.0.25 (32 bit)
The applet uses a JNI dll compiled with x86.

Recently it was updated to run with JRE 1.6.0.31 (32 bit). The jar files are now being compiled with JDK 1.6.0.31
Here is the object tag
<!--[if IE]>
<object
name="myApplet"
classid="clsid:8AD9C840-044E-11D1-B3E9-00805F499D93"
codebase="http://java.sun.com/update/1.6.0/jinstall-6-windows-i586.cab#Version=1,6,0,31"
width="100%"
height="90%">
<![endif]-->

<!--[if !IE]>
<object
id="myApplet"
name="myApplet"
type="application/x-java-applet;version=1.6"
width="800"
height="600">
<!--<![endif]-->

I perform the following steps:
Launch the html page that loads the applet.
The applet loads fine
Refresh the page (F5 or clicking the Refresh icon)
The applet loads as expected, but within about 10 seconds the Java console closes.

(The Java console does not have any exceptions/ error like messages when logging and tracing are turned on via Java Control Panel-->Advanced)

This problem does not happen on a system that has JRE 1.6.0.25
The problem does not happen in Firefox 12. It does happen in IE 8, IE9 and Chrome.

Any suggestions on what might be wrong or how to debug would be appreciated.