Effective dps (e) is based on fight length, DPS is based on active time. There are other factors in there as even someone with 100% activity may not have them equal.
For example: Total Damage: 10,000,000 Fight Length: 5 minutes Activity: 96%
DPS (e) = 10,000,000/300 = 33,333 DPS
DPS = 10,000,000 / (300 * .96) = 34722.22
Basically if you did 200,000 DPS in a ten second period and stopped (or died) for the rest of a 5 min fight, your DPS would be very high, your effective DPS would be very low. Also, last I checked, Recount displays DPS (I haven't used recount in a long while), while Skada displays effective DPS.