Here is the straight dope on this set. If we are talking about the 10th Anniversary PE set. The Berkshire locomotive that comes in that set is a very nice locomotive, but it is not its full scaled cousin. That being said, it will run and run and run, but even the best electronic items can have moments of slowing down. I suspect this has to do with the internal electrics more so then the track. Though my PE ran nice, she also had periods of running somewhat slow.
I believe this is normal. However, if she bucks or has periods whereby she actually stops, then that is not normal and needs to be addressed. The simple solution is to contact the retailer where the set was purchased and advise them of the issue(s). See if you can exchange for another. Most reputable businesses will do so because they want repeated business. If that does not work, then contact Lionel under the warranty. They may exchange/repair the issue. The track can get dirty while on the floor from smoke settling and dust. This can cause slow downs as well.
These mid range sets are nice, but they are not, as I stated, like their larger up scaled cousins. Also, as far as those extra cars, the cars are lighted as everyone obviously knows. That means they are also requiring power. Which translates to less power for the whole affair when adding them to the original three that come in the set. One idea is to add a more powerful transformer and wire the whole track to keep voltage constant and consistent throughout the whole track/oval. That way she should run smoothly even with the addition of a few extra cars.
Best of luck.
Pete