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It is just as Jeffy says.
When you're dealing with big, often popular addons - or even small addons to some extent - you're literally running tens upon thousands of lines of code that've been delevoped individually. While Addon A and Addon B and Addon C have all been constructed to work flawlessly with WoW, maybe an actionbar-changing script in Addon A interferes with a buff-hiding script in Addon C. Or maybe there's a bug in Addon B, the pet randomizer addon, that makes the game behave erratically when Addon A is loaded. Disabling any of the conflicting addons gives the impression that that addon was the culprit; however it doesn't mean the addon created the issue in the first place.
As far as I know, Carbonite does absolutely nothing regarding tooltip fade time, lending credability that, if you would run with Carbonite as the only active addon for a while, you would encounter no similar issues.
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