Not sure why. The 14th Amendment seems to apply to both cases.
The difference is that in Bush v. Gore, the U.S. Constitution clearly gives Congress the authority to lay the ground rules for Presidential elections. When the Florida Supreme Court issued a ruling calling for a statewide recount that extended beyond the original certification date for the Electoral College, the U.S. Supreme Court had no business getting involved. The original certification date should have stood, and if Florida couldn't get its act together to meet that deadline (for whatever reason) then their electoral votes simply would not have been counted.