This has been a long standing issue, and still is. There are multiple issues on Github regarding this problem, and most of them boil down to the same thing: Pigments is slow. We are aware of this problem, and we are sorry.

To clear things up a bit, I decided to bundle links to all issues into one master post. One issue might contain more information than another, so I've tried to sort them by amount of messages and "usefulness".

#125 (38, cpu timeline, dummy file, insights)
#363 (5, script to trigger issue)
#275 (22, insight: might be related to Anti-Virus)
#116 (6, cpu timeline, insights)
#366 (1, only occurs on some markers)
#188 (19, cpu timeline)
#330 (16, commands, stack trace)
#308 (14, stack trace)
#175 (20, dummy project)
#43 (16, dummy file)
#95 (5, dummy file)

Mostly "me too", "same", +1, 👍, confirmations:
#293 (9)
#121 (6)
#340 (5)
#306 (5)
#202 (4)
#235 (2)
#159 (2)
#360 (1)
#367 (1)
#421 (3)

I'd like to ask you all to post any more future information here, to keep it somewhat manageable. Thanks.

Sidenote

As some of you might have noticed, @abe33 seems to be focused on another project. Because of that, maintenance on pigments is slowed down (update: has been brought to a stop).
In the meantime, I'm trying to keep the issues clear, the labels accurate, and to solve small issues. I don't think I'm able to solve this (major) issue on my own, that's why I'm trying to make it easier for others to help.

General recommendations

If the latest version doesn't work, you could try downgrading pigments by uninstalling it, and reinstalling a specific version via apm:

apm install "pigments@0.38.0"

If pigments still doesn't work for you, color-picker or highlight-css-color might. A (prehistoric) version of pigments, known as atom-color-highlight is still downloadable too. No guarantees are given for any of them to work.