[seec]

It wasn't even well known until very late into the 2000s (even early 2010) when Apple actually started to make a lot of money and got a lot more scrutiny.

Because it is pretty simple, you don't really care about a struggling company or one that just gets by, even if their marginal tax rate is lower than it is supposed to be, since there isn't much to be taxed the difference is minimal in any case. However, if the company is extremely successful and makes big money the difference is absurd and it actually becomes unfair for everyone (both other companies who have to play by the rules, and citizens who get taxed more than a filthy rich corp).

And this is the real reason it "became" a problem and took a while to resolve. Had Apple stayed a relatively small company with small sales numbers in the EU (and thus small profits) the deal would have probably not have much scrutiny and even if it had, it probably wouldn't have gotten any focus. It would have cost more money in legislators time than it would have brought in anyway, even though the deal was fundamentally unfair. But life is generally unfair, so it doesn't matter that much.