According to the official help site,
"Ink signatures use the default color of Pencil tool markups. To change the color of the signature, right-click the Pencil tool in the Comment & Markup Toolbar. Then choose Tool Default Properties, and change the color in the Appearance tab."
I had the same problem, spotting your question along the way. Finally I stumbled across the above.
I tried to find a better means of accessing the pencil tool's color, but this is the only way to change it. While I understand that this software isn't supposed to be Photoshop or anything, this method of changing the pencil color seems completely arbitrary at best. But, on the other hand, at least it can be done.
Hope this answer got to you in time to be useful still!
~Malcolm
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Source: | http://help.adobe.com/en_US/Acrobat/9.0/Professional/WS58a04a822e3e50102bd615109794195ff-7d48.w.html
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