Hi Jason,
I often recommend people to do the Gate technique for at least 30 days. Listening to Frank on MP3 or on CDs never grow old. But most importantly, it will become such a part of you that you can pull it out of your "tool box" any time you need it, without referring back to the book or MP3. Even though you may feel you have done the Gate enough times, just stick with it. It'll pay you dividens.
Many of us experienced PA/Eufeeling throughout our lives. That's why it feels so natural to go back there. The beauty of it is that we can go to PA/Eufeeling almost "at will" with QE now.
Once you are safely nestled in PA/Eufeeling, letting go of your "lingering" negative emotions will be easier, too.
I also sense there may be an expectation issue here. An attachment to a certain outcome.
In this case, for the certain emotions to evaporate instantly.
It does evaporate. But the attachment could keep it from happening. The attachment may also allow it to come back.
I'd take each time the negative emotion surfaces as another chance for me to QE. Even if the same emotion keeps coming back, take it as another opportunity to QE. You are so lucky you're given so many opportunities, don't you think?

You might also be "interfering," "analyzing" or "judging" the process too much. When you notice anything is lingering, what are you thinking?
"Why is it not going away?"
"Am I doing this right?"
"Maybe, I'll never get over this."
All these are the signs of autothinking. You are pulled right into the devil's (ego's) workshop.

How do you stop this? By observing. Observing without analyzing, criticizing, interfering or reasoning.
May I also suggest you read Beyond Happiness, when you get a chance.
Beyond Happiness goes beyond techniques.

Happy Gating!