Was the A/C on? My 1999 328I started to have the same type of noise and after thinking it was the engine it ended up that the A/C compressor was going (and still is, getting it replaced next week) and making loud tapping noises.
Hope this helps,
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2002 Slap National SQ Champion Pro Street 601+
2003 Slap National SQ Champion Pro Street 601+
2004 Slap Expert Class 5th Place
2005 Slap Expert Class 2nd Place
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