That power doesn't pulse for me and I don't remember it ever pulsing. The only thing I did with power customization was to set the no Fade on for the cloak (stealth +def) power so I could see my character all the time.
I have noticed on some powers (talking more than just DA here) that the particle count has to be a certain level before they look right. I know some of the fire armors appeared to pulse when I had mine set to minimum and it got a lot better when I raised it back to normal. Something similar maybe?
Or maybe it's supposed to and I just don't see it. A definite possibility for me.
I have my stuff set to the higher levels (ultra mode). It's not all jacked up to maximum but nothing is under normal either and most things are in the upper quality tiers.
What happens is that, when the power is active, the character itself regularly deepens in color to nearly black and then back to normal. I can't play in the creator itself to test this since it just cycles the "activating" animation over and over so I have to make changes and then come back out to test, go back in, etc. I get the same effect whether it's set to "No Fade/Pulse" or just "Custom Color".
If no one else has any idea what I'm talking about, maybe I'll try to capture it with Fraps or something. If I can't fix it, I'll just reroll into a different power set as it's visually very annoying to me.
Mine definitely do this too, despite the setting. It's not just you.
Where to now?
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Ah, well, that's disappointing. At least I noticed by level 3 so no harm done in starting over and picking a less obnoxious power set. Thanks! 
Made a DA character last night and, despite setting it to "No Fade/Pulse", my character definitely pulses to nearly black and then back to normal every few seconds. Tried various things at the tailor to be sure it wasn't just a settings issue but, nope, he pulses.
Working as intended? Are other people able to avoid this effect? Forgot the name of the power but it's the first one (+Res toggle).