Does GPG still own Supreme Commander's IP rights or it belongs to SQUARE ENIX?
And I wonder how Chris Taylor/GPG got Total Annihilation's IP rights again?

Thanks guys!

SE owns the rights and GPG doesn't own the rights to TA at all.

Supreme Commander 1/FA was released by THQ, how SE could own the rights?
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Somehow, I heard from some where TA's trademark/IP rights/copy rights (I forgot which one) back to Chris Taylor's hand...

Because they bought them... CT does not own TA.

The Intellectual Property for TA is currently with Atari btw.

where I can find the reports that SE bought SC's IP rights?

Here is the trademark filed with the US Patent & Trademark Office:
http://tarr.uspto.gov/servlet/tarr?regser=serial&entry=78325032

Here is a record of the transfer of the trademark to Square Enix:
http://assignments.uspto.gov/assignments/q?db=tm&sno=78325032

Here is the legal page of Square Enix:
http://na.square-enix.com/legal