I'm 1750sp unbuffed (hitcapped, 18% crit, 200haste off the top of my head). With only Inner Fire up I pull 2.7k on a boss dummy. Also I'm not 100% on this but, isn't part of the reason Shadow sucks on dummies is because they are mechanical and ignore our Devouring Plague (which accounts for something like 11% of my DPS or about 300dps).
It could be some minor problems with her rotation stemming from the lag you mentioned, or it could be something she is forgetting to do (I'd actually suspect the lag to be honest).
All that being said I was first overall tonight through Naxx25 - our top mage wasn't present but our top aff lock and 2 surv hunters were there, and on at least 4 seperate bosses I was first on dps above them all as well (so it's not just trash). Part of that is that I am very attentive and constantly tailoring my rotation throughout the entire 4 hour affair while I think they get lazy on trash or even on the simpler bosses (by contrast, our Arc mage always beats everyone on everything).
About the wws which was posted on the first page. That was, if iamrite, on patchday with the bugged Misery.
Most of the SP did there 5.5k Dps on patch(myself too).
Her Gear is far away from being best in slot ,so her dps seems not too bad.
To our utilities:
-Misery : Can be replaced with imp FF but moonkins doesnt want to cast it coz its a dps loss for them. Misery wins!
-vE : Its unique ...its our best survival Spell for us... healer love sp coz we need less heal than others, iE sarth 3D with the second(?) drake we cant easily outheal the inc. dmg from the debuff (not the "meteors" ). The group heal is weak, to weak imo.
-Replenishment: Hunter will never specc for that so there are only Rets and Spriest left. I guess most raid will bring 1 Ret since stacking melee isnt a good idea. And with deathknight there are only a few spot left.
A proper raid will always have 2 replenisher to have the best effort out of this buff and that one will be us.
We can heal for a short time if its necessary. Can save someones life with shields and and and...
Simple answer for OP, she needs to get better gear and regem away from spell penetration. She also needs more haste.
The set bonus for 4p t7.5 is worthless, she should never wear more than 2 pieces...preferably gloves and shoulder. Spellpower/spirit or crit/spirit gems are what you use to get the 2 blue gems needed to activate the meta, which should be the 21crit/3% increased crit damage.
Her gear and dot uptime need work, that is basically why she is doing subpar dps. If she doesnt already, she should also use Quartz cast bar. That will pretty much solve her fps issue.