Lets get to the subject of jumpscares.
Jumpscares do work if they are subtle and work with the narrative. For far too long I have seen too many custom stories turn from an area where a man can express their creativity (Through The Portal being a fantastic example) into a massive field of bile where the only motivation is to get a cheap reaction at the cost of quality.
If you look at Cry's videos, you can see that he rarely does Amnesia anymore, why? Because of this sad descent. I am not saying that PewDiePie is bad or that I despise him, in fact I respect his success, but he has influenced the community for better and for worse. Better because it is showing an open window of opportunity for people who want to get into the games industry, while on the other hand, there is the aforementioned bile.
The best scare is created by creating an eerie effect via atmospheric sounds with quick pokes of potential danger. Remember the rooms in the main game before descending into the refinery? You wasn't in danger at all, yet because the game paces itself well it keeps you on your knees. Repetitive flying naked guys was a but junky yet fun for the first few times, but now it's just one of the main warning signs of a bad custom story.
Here is a little video that should help you.
TL;DR - Pacing is the enemy of the player, in a good way. Subtlety and fear of fear is much more powerful than startles themselves. Want a good example?
This should do