This article here:
http://www.canadiandriver.com/articl...3_5-series.htm mentions,
"In 1999, the 5-series wagon, which had disappeared after 1995, returned to the line-up. Dubbed "Touring" models, E39 wagons were available with either the 2.8 litre (and later, the 2.5 litre) and 4.4 litre engines, and were badged 525iT and 540iAT, the "A" in the latter's name denoting the 5-speed automatic transmission that was the only option for getting the power to the road."
Touring version or not, it does seem that the "A" corresponds to an automatic transmission so I have no idea what happened with your 5-speed Brian.