Copter was sluggish and didn't seem to follow commands

I have a S1000 that I have an original pixhawk (running Copter 3.5.2) and a companion computer that can upload missions to the pixhawk. It has been quite reliable and flown extremely well. I have a night-time waiver and have started to experiment with flying it at night–the first flight went well but on the second flight, it seemed off. The pixhawk would accept missions but didn’t go to the waypoints it was supposed to, etc. I also noted that on takeoff (which is an automated sequence of arm -> switch to guided-> send takeoff command -> when at desired altitude switch to auto) there seemed to be a much longer delay between the end of the arm tone and when the motors spooled up to takeoff. At the end of the flight when the RTL command was sent, it also seemed very slugglish to respond. It was like it acknowledged it, but then took 3-5 seconds to respond and actually do the RTL.

Normal Flight
Odd behavior

Could I by chance get some guidance on where or how to invest this in the logs? I attached two logs-- one of the flight just before the flight with the odd before and the one of the add behavior flight itself.