Here is a mode2 version of v31, this will work in both the M3 and MK4, download and burn, then redo the update, hopefully it will fix your problem.

Rapidshare
http://rapidshare.com/files/161127862/v31_OEM.zip.html

Megaupload
http://www.megaupload.com/?d=5N2H2Y50

Burn at either x1 speed or the slowest rated for the blank CD.

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Sept 03, M3, Silver Grey. Retro-fits: Modded Mk4 DVD Drive, OEM Bluetooth, VR Control, Rainbow Speaker Upgrade, Sony SOT Amp, HK Sub, CCFL, Intravee II, NightMode.