How can a website detect thumbprint?

Awhile back I signed up for a free service.

Because it's free, for obvious reasons they put a cap of one account per person. I tried to evade this by doing the following:

--Anonymous proxy

--new browser (Firefox instead of chrome)

--cleared out cookies

yet somehow they were able to detect I already registered

But shortly after registering on new computer and different ISP worked.

How would this have been possible? People just assume that changing IPs and deleting cookies eliminates all traces, but somehow this website was able to still know. Is there a type of stealth malware that embeds itself into your system or something when you view certain websites and thus permanently marks your system.

The final test would be to reformat the system, use new ISP, new IP, etc and see if it works