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My 2003 E39 520i had exactly the same symptoms as described.  After overnight or longer non-usage of the car, the aircond will not blow, and therefore not cold when car started.  After 5 to 10 minutes with engine on, the blower and aircond will spring back to life.  I mentioned this to a few aircond shops but to no avail.  I put up with this inconvenience for a good 1 to 2 years when one fine (hot) day it just will not switch on, even after more than 30 minutes of driving.


In desperation, went to another aircond shop (Penang), mentioned the symptoms and before I could finish, the shop man finished describing the symptoms for me (correctly) and diagnosed the problem - need to replace the "blower regulator".  It is a small item under the dashboard on the driver's side.  It took 5 to 10 minutes to replace.  So far so good for the last 6 months.  Costs me nearly RM300 for replacement "blower regulator" and labor.


Hope that helps.


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