I had a similar problem getting mozilla 1.4 to see my java(1.4.2) plugin after I installed repeatedly. What I had to do was go into preferences --> scripts and plugins --> uncheck enable java for navigator, close mozilla, open mozilla, then check enable java. After I did that it recognized my java plugin. WOrked for me. Also make sure you are creating a symbolic link to the java plugin. Another thing you may need to do is to make sure you are putting plugins in the correct mozilla plugin directory. When I was running mozilla 1.2.1 I had to put plugins in /usr/lib/mozilla/ however after I installing Mozilla 1.4 I must use /usr/local/mozilla/plugins (the mozilla install directory). Hope this all helps.
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