The "Scrubs" soundtrack featured on the streaming services is different for the same reason that "WKRP In Cincinnati" was completely unavailable for decades after it aired — and so, the situation could be worse.
The show's rights owners had to swap out many of the songs used on "Scrubs" before making it available online because they didn't have the songs' streaming rights. Basically, the producers of "Scrubs" committed the sin of not predicting the streaming revolution.
"Scrubs" debuted in 2001, back when Netflix was still just sending DVDs through the mail (it wouldn't launch its streaming service until 2007). That is to say that when the show's producers were negotiating the rights to the cutting-edge pop songs they wanted to feature (one of the reasons fans and critics loved "Scrubs" so much), streaming wasn't even a thing yet, so they didn't know to negotiate the rights for it.
It's a near-perfect repetition of what happened with "WKRP in Cincinnati." That show, too, got loads of acclaim when it first aired for featuring popular, edgy music. However, years later when home video and DVD boxed sets became a huge new source of revenue for old shows, "WKRP's" rights holders found themselves unable to capitalize on it because they didn't have the rights for this new medium. It was only a few years ago that things were finally worked out and a DVD release happened, but it was arguably too late — boxed set fever had passed, giving way to streaming as the rerun format of choice.
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