EPA 8260 would be using Purge and Trap, so inlet maintenance is pretty much not needed unless you are foaming a bunch of samples.
What Purge and Trap are you using?
Does it have a moisture control unit?
If so, when is the last time you cleaned the moisture trap?
What split ratio are you running and what are your inlet and transfer line temperatures?
If high boiling compounds build up in the moisture trap(they will condense on the walls just as the water will) when you bake the trap at high temperatures you can possibly be pyrolizing those into a thin carbon film on the walls of the moisture trap. This then acts similar to a chromatographic column, where the lighter compounds pass through while the heavier ones get trapped.
Also if you have the EM Voltage too high it can cause similar problems. Check out this app note:
http://www.chem.agilent.com/Library/app ... 0603EN.pdf
Page 11 describes the fluctuation of internal standard areas versus concentration of standards. It also has quite a few good tips on running purge and trap.
Higher boiling compounds can also be affected if your analytical trap becomes contaminated and is holding on to them more strongly than before.
This sounds more like a purge and trap problem than a mass spec problem, though it can be mass spec related too.