Yeah, the MACO engine's a little slower at warp and faster at slipstream, that said, if you did notice a change, it could be your setup, skillwise, or if you're flying an Odyssey, and you removed one or more of the Odyssey consoles where before you used all three, if I don't recall incorrectly you lose a driver coil set-bonus as well.
Actually, looking at your numbers, looks like the Borg engine speed "stuck" when you switched engines and refreshed down to the correct MACO speed. I'd have to check the driver coil bonus on the MACO engine, but that look like about the speed you'd have if you had the driver coil bonus on top of the Borg engine.
Were you by any chance already at full speed when you switched? Did you change maps any time before losing the higher speed?
My driver coil is at 9 and I haven't re skilled. I was using the Chimera Heavy Destroyer and had no driver coil buffs from D'off missions. If I had had them my speed with the Borg engines would have been much faster than the 20.93 I was getting.
My fleet was having a discussion last week on their forum on how to get the most from the tour the galaxy event so I had been flying around Fed space, Sol down to the Eta Eridani Sector Block and making notes of the numbers, coming to a full stop and then swapping engines.