Theres a few things that can throw recount off by quite a bit.

Fight time can be thrown off by multiple things, for example:
-Pulling with your tank several seconds before you start DPS.
-Some classes have a slow ramp up time, you simply can't achieve good DPS in under 20 seconds.
-Recount will keep tracking your damage til you stop so if you stop dps and a DoT ticks for another 10 seconds it will count that time against your DPS. (Dummies)
-Short fights like Heroic bosses can be skewed wildly by lucky crit streaks. I know on Loken I have broken 11K DPS on a mage that managed to score 70% crits with awesome proc luck when his avg on that fight is usually more in the 8-9K range.

Also keep in mind that raids are quite a bit different than heroics in other ways. You can dump a TON of +hit in heroics to pic up additional DPS stats and your cooldowns can last an entire fight, also proc based classes may not get any love at all.