If you enable “Handle triggers separately”, stagger won’t work anymore and all class items will get triggered at the same time.
Hmm… I cannot reproduce it locally. Can you send me access? 
I just contacted you via private message and sent you login credentials for the demo page.
Thanks for access! Everything seems to work as expected. If you want to run staggered gsap timelines when in viewport, you should use batch instead.
Reference:
Panel Setting:
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Hi Daniele
It does indeed look good now. I’m sorry – didn’t know about this behavior of gsap. After knowing it & digging deeper into it, I just found the same question on their forum: why stagger is not working in scrollTrigger? - GSAP - GreenSock
Thanks for taking your time – definitely no bug 
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Hehe, I came across it recently too. That was the reason why “Batch” has been added as feature 