I am no expert in this area however I remember when bluebird built his cervia he used a 550 motor and mentioned this:
Now the motor I have installed into this model is a 550 motor. When we tested it ‘free running’ coupled to nothing, the motor was sitting on the bench and we ran it at 6 volt. According to the book we have and the information sheet, for this particular motor, at 6 volt; she should draw between 0.4 and 0.5 of an amp and she should rotate in the region of between 15000 and 16000 rpm.
Assuming that there is no load on your 540 and assuming a similar unloaded current draw I would expect to see something similar to the following:
0.5 amp draw
4 amp/hour battery
4/0.5=8hours run time
Now nothing is perfect so I would assume less run time than this maybe 6 hours
http://www.jaycar.com.au/products_uploaded/SB2496.pdf are some specs for a similar battery
Given this I would assume either the battery is on the way out or it was not actually fully charged.
Given the batteries age its also important that they are stored correctly. I have assumed the battery is a sealed lead acid and I believe these should be regularly "cycled" to keep them in top nick
By cycled I mean discharged and charged every so often.
Hope that helps,
Tim
[Edit] Not wanting to hijack this thread but I'm curious as to how low people discharge a 6v battery too, I'm thinking you probably don't want to go below about 5.25V but im not sure.