I also have a 1999 540i6 and used Redline ATF and works fine... Just noticed a small leak every 6 months or so, don't know if its related to the atf tho.. Apparently if you call Redline for trani they recommend ATF even in the manual trani. The rear diff we used redline synthetic gear oil.
'99 BMW 540i6 (black on black)
'99 Lexus Rx300