The downloaded episode has no music (e.g., silent scene transitions). Fix: You likely purchased a “streaming master.” The only way to get the original music is to rip the DVDs. iTunes/Amazon versions occasionally still use altered tracks.
The only ethical, safe, and high-quality way to is through authorized digital retailers or by ripping your own DVDs/Blu-rays. Here are the best options: Download Scrubs Complete Series
If you prefer streaming over purchasing, the original 2001–2010 run (Seasons 1–9) is widely available: The downloaded episode has no music (e