Thats odd, having different certificates should just show multiple security dialogs (one for each certificate) but there have been occasions were due to some buggy vm's it would freeze like you explain above. One would expect Oracle/Sun to have fixed these sort of issues by now.
Besides you should never need more then one certificate for your application/game anyway, if you don't need to sign your own jars, just use LWJGL's certificate or if you are signing yourself, just sign all the jars (including lwjgl jars) with your own certificate. Multiple Security dialogs just annoy users.
Just curious, were any of the certificates set to always remember (i.e. the checked box on the security dialog selected in a previous run)?
Also when you say crash the plugin do you mean that it would just freeze or actually crash?
I know you've fixed the issue now, but it would be useful if you could just upload an example of the crashing applet somewhere to allow further testing just to make sure its not the appletloader or if there is some workaround that can be used to stop the crash.