Not really sure. It could be the aft end of the fuse resulted in more drag due to the different shape or the fact that the SR-71 had camera and sensor ports along both sides of the lower fuse while the A-12 had them running in a line down the center of the bottom. Here are a couple of excerpts from my source:
Early in 1963, the A-12 made its first flight with two of the J58 engines. During this year, the program experienced its first Blackbird loss when an A-12 crashed near Wendover, Utah on May 24th. Also, the aircraft made its first flight at Mach 3.2, the speed that the aircraft was intended to fly at in November.
The estimated maximum speed of the aircraft is Mach 3.2 and some sources say that it can accelerate to Mach 3.5. The estimated maximum altitude is 85,000 feet but some sources say that the SR-71 can fly up to 100,000 feet and can probably go even higher.
Here's another interesting "tidbit":
The SR-71 is the fastest and highest flying production aircraft in the world. The only aircraft that is faster is the X-15 that can reach a speed of over 4,000 mph. The only aircraft ever to come close to the SR-71's speed besides the X-15 is the Russian MiG-25 Foxbat. The MiG-25 could only reach speeds of over Mach 3 for a few minutes. The Anglo-French Concorde is the only aircraft besides the SR-71 that can fly at supersonic speeds for hours at a time.
Last edited by Hydro Junkie; 02-19-2018 at 08:38 AM.