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Can you post screen shots to better explain what you are referring too? I don't have JB on my S3 but I have it on my nexus 7 and the widgets look fine to me. I'm not sure what you define as "normal".
It is a known issue and there is a fix for those who are rooted.
I'm rooted, what's the fix?
As you noticed it is a transparency issue.
Here is the fix:
http://forum.xda-developers.com/showthread.php?t=1894633

I have this exact same issue!
I'm running JB 4.1.1 on my international 4G (GT i9305), and encountered this problem.
Have been using Apex on my previous phone - galaxy nexus - without any hickups!
Now I upgraded to an S3 and have the same problem as op.
Is there any other workarounds that anyone knows of, because I haven't unlocked or rooted my S3.
Any help is appreciated, as I love this launcher (just the ability to re-arrange icons on a screen without having to go into edit mode pays for itself lol)