It is true that for the first fifteen months or so after President Obama was inaugurated, the White House never 'authorized' his signature on certificates for Eagle Scouts (or Quartermaster or, presumably, Silver Awards for Venturing).
That changed in late spring or early summer of this year when his signature was added. Scouts earning the rank of Eagle BEFORE that time had a blank above President Obama's signature.
However, he's NOT the first President to do this.
President Clinton didn't sign certificates for quite a while after taking office . . . and when he agreed to sign them, the White House 'requested' that the standard certificate be changed so that it could be signed not only by the President of the U.S. (the honorary President of the BSA), but also by Hillary Clinton. Yep.
That's been 'cleared up' and his signature now appears on Eagle Scout certificates.