Hey I found a work-around solution to use WS on Premiere CS6. It's not perfect, but this is how I did it:
1. Make a new sequence (Let's stay 'Sequence 01') that matches the dimensions of the footage you want to stabilize.
2. Place the said footage into the timeline of 'Sequence 01' and run WS. It should work.
3. Then, place 'Sequence 01' into the timeline of your main sequence and scale however from there.
Let me know if that helped. Cheers!
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