Skada calculates whats called DPS(e) which is DPS effective. From the start of the fight to the very end it calculates your DPS nonstop.
Recount calculates DPS. When you stop DPSing for a period of time, Recount will stop the timer and hold your DPS at whatever number you're at until you start DPSing again.
For example, for a fight like Immerseus or Fallen Protectors they both will have around the same number since there really isn't any time when you aren't DPSing. For fights like Galakras, the tower teams DPS will be lower on Skada than on Recount cause Skada will keep a running timer whereas Recount will stop until you start DPSing at the top of the tower again.
To use some numbers as an example for the Galakras fight...if you did 150k dps for 60 sec on the ground and then you have to run up the tower which took 10 sec and you did 150k dps for 30 sec there too, Recount would ignore that 10 sec gap and would show you did 150k dps that fight. Skada on the other hand would take that 10 sec into account and say you did about 135k.
Thats the difference. These methods also go for HPS...Skada calculates HPS(e) and Recount does HPS.