From: Sydney, Australia
No, that is not the problem. Let me explain, hopefully I will do a better job this time :)
As a starter, you fly a fighter class vessel and engage in combat with pirates flying fighter class vessels too. These pirates sometimes hit you with focus fire, which causes around 40 points of damage, which is enough to take down shields by, say, 15%. All good so far.
After a while, you advance to a Corvette class. You now have far stronger shields and stronger guns. Occasionally, you will still engage pirates in a Fighter class vessel, same as before, when you were still in a Fighter yourself. These pirates will sometimes hit with Focus Fire, still all good. But suddenly, this same vessel that was causing ~40 points of damage is now causing more than 120 points of damage, and still taking off 15-20% of the shields with that hit.
It looks to me like, purposefully or not, the damage from Focus Fire is some percentage of the target and not a function of the firing vessel. Whether or not this is the case, I have no idea, only speculation. However, I do know it is annoying. I expected that once I get a Corvette, I will barely take any damage from Fighters and be able to swat them out of the virtual sky. Instead, while it is slightly easier to kill these Fighter-class-pirates with a Corvette, it is not MUCH easier and can still leave you pretty damaged.
Hope this makes sense.