You might want to take a look at this articles:
Pelican BMW Technical Article - Alternator Replacement - BMW 325i (2001-2005), BMW 325Xi (2001-2005), BMW 325Ci (2001-2006), BMW 325ti (2001-2004)
http://www.pelicanparts.com/BMW/techarticles/101-Projects-89-Alternator/101-Projects-89-Alternator.htm
These may help answer some questions you have in regards to trouble shooting your alternator issue. If not you can post a comment and I am sure a technician may be able to better assist you with your issue.