I've got the same problem. I have a track that has scratching and popping in MC but NOT in WMP. I have even opened the file with Media Editor to see what's there and when I play through Media Editor the scratchy pop goes away. I've tried changing output modes and other settings but no dice. I've also tried converting (via Media Editor) to WAV and listening to it, but it still has the sounds.
Using AC97 sound on my Gigabyte MB, so I'm trying to find updated drivers for it (although since it plays fine through WMP, I don't think it's the driver).
Media Center Registered 9.1.271 -- C:\Program Files\J River\Media Center\
Microsoft Windows XP Workstation 5.1 Service Pack 1 (Build 2600)
Intel Pentium 4 2376 MHz MMX / Memory: Total - 1048 MB, Free - 649 MB
Internet Explorer: 6.0.2800.1106 / ComCtl32.dll: 5.82 (xpsp1.020828-1920) / Shlwapi.dll: 6.00.2800.1226 / Shell32.dll: 6.00.2800.1233 (xpsp2.030604-1804) / wnaspi32.dll: 4.71 (0001) , ASPI for Win32 (95/NT) DLL, Copyright © 1989-2002 Adaptec, Inc. / Aspi32.sys: 4.71 (0001)
Ripping / Drive F: Copy mode:ModeBurstBigBuffer CD Type:Auto Read speed:Max
Drive G: Copy mode:ModeBurstBigBuffer CD Type:Auto Read speed:Max
Digital playback: Yes / Use YADB: Yes / Get cover art: Yes / Calc replay gain: Yes / Copy volume: 32767
Eject after ripping: Yes / Play sound after ripping: No
Burning / Drive G: LITE-ON LTR-24102B Addr: 1:1:0 Speed:24 MaxSpeed:24 BurnProof:Yes
Test mode: No / Eject after writing: Yes / Direct decoding: Yes / Write CD-Text: Yes
Use playback settings: No / Normalization: None