Barring evidence to the contrary, yes there were two certified copies. The DOH even told Ivan Zatkovich how they were made.
“A representative of the Hawaii Department of Health described how the copy of the Obama Birth Certificate was produced. She stated that the copy of Obamas birth certificate was produced by taking the original paper birth certificate, which was black printing on white paper. The original is then placed on the photocopy machine and that image is copied onto green safety paper. That green copy is then stamped, dated and signed by the State Registrar.”
http://www.ecompconsultants.com/news/Obama-report.pdf
Fair enough.
The LFBC posted by the White House only has a black stamp. We know it's only black and not multicolored because the safety paper background is green, so a multicolor stamp would be visible.