Plugin: 3rd Party applets not working

I have an internally developed applet that requires us to install the Plug-In under our IE 5.5 and 6.0 browsers (about 10,000 of them). Upon doing that, I will now have a handful of 3rd party applications that employ applet technology, and that will not work with the Plugin (lots of classnotfoundexceptions being floated around). The only way that I've found I can make these applets work is to turn off use of the Sun Plugin within IE. I am wondering if this is a plugin, or vendor, problem.
* What is the basic problem here?
* Is it that these other 3rd party system are written to an older spec and the 1.4 plugin will not support them?
* Is Sun's plugin not backward compatible with older applets?
* Did these vendors screw up in some fashion in their applets or HTML?
* Is the whole idea of applets inherently flawed?
What are other folks doing to get around these incompatibilities?

I don't your exact problem with the ClassNotFoundExceptions, but it may be because those applets are using Microsoft specific APIs that caused all the lawsuits to fly.
I have had success mixing applets requiring the Java Plug-in with those that need or run best under the Microsoft JDK, as follows:
When the Java Plug-in installs, do NOT take the option that makes it the default plug-in for the browser.
In your web site:
Launch the JDK 1.4 applets with the OBJECT tag.
Launch Microsoft specific applets with the APPLET tag.

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