Error : Could not initialize class com.altera.systemconsole.internal.plugin.jtag.aji

I'm glad you've got it working again.

The error message occurs because that Java code is unable to load it's native library, JtagJNI.dll.

What I suspect happened here is that your path had somehow made windows load the wrong versions of the native library - one which is not compatible with the Java - or that that DLL found the wrong version of a dll it depends on. (The windows DLL loading rules are byzantine, and Java doesn't really provide any good ways to override them)

But I'd like proof before jumping to conclusions.