Yesterday morning my 2007 e60 wouldn't start. Ended up jumping it and that solved the problem - at least I thought. While driving to work (approx 2 miles) I noticed that the clock needed to be reset and the service light was on. I set the clock and didnt give another though to the service light.
After work the car started fine but the clock needed to be reset again and the service light was still on. I figure it can be two things:

1) the battery was completely drained and the 2 mile trip to work was enough time for the alternator to re-charge the battery which is why the clock reset again
2) the alternator is bad which is why the battery died the first place.

The car is on CPO but if its the battery its not covered. But if its the alternator, it would be. Any ideas?

2 miles is definitely not enough to charge the battery. I would drive at least 20 miles, or use a charger.
Do you always drive this short distances? Then it is normal that the battery is drained.

^^ what he said. exactly.

I did try charging it with a trickle charger over-night but it didn't work. Car only started after I jumped. I suspect it was because battery was drained??

a trickle charger won't do jack for a drained battery unless you leave it on charge forever and ever. its probably a bad battery unless its the alternator or some electrical short draining the battery. most likely it's the battery though. just get a new battery at any auto parts store.

battery tender is a good option to keep the battery "healthy"...but I feel like we shouldn't have to do this...seems like an issue with the E60 for sure!

The "Service and Warranty Information" booklet (ref pg 16) for my '06 E61 includes the following statement:

Additionally, the car starting battery (SLI), if "cold" in the morning, will have a bit less useable capacity, and, if "warm" in the afternoon (car sitting in the Sun?) may have a bit more useable capacity.

HTH,
Jim / crewzer

If alternator, your would not be start at all or i would start but for short time only, like 30 sec.
Replace battery, mine did same clock would reset itself.

I'd vote for battery. CEL could be other systems that have shut down due to low battery. Time and date resets are strong indicators of bad battery. How old is it? My 2008 has had two batteries so far and it is driven very little as well. You do need to take it for a nice long ride with all accessories off to recharge the battery you have if it will hold a charge.
A trickle charge is useless. You need to charge overnight with normal settings (non trickle) for your particular charger. Mine is 100A for quick start, 15A for overnight and 2amp trickle or maintain cycle.
As 'phlfly' stated, your battery wouldn't have any life if your alternator is dead.

Today my battery was so drained out that it couldn't last for more then 30 sec. without plugged in cables to another car. For the moment I thought it could be the alternator but I doesn't make sense. After some time we disconnected the cables and I did at least 20 miles around. Right now it starts but tomorrow I will go for a new battery. 2005 model, first battery, mainly on highway. I think you should replace for battery too.