The tone you hear means a train dialed the dispatcher and is trying to call them. It's basically like a "phone call". They punch in a (usually) 3-digit code on their engine radio. They can also call up mechanical help desks, PTC (Positive Train Control) help desks, and the like depending on what's going on in the field.
What type of scanner or radio and antenna do you have? Moving your equipment closer to a window can typically help. Like ElevatorsAndRadios above said, an external outdoor antenna will greatly help, and these can usually be found fairly cheap on websites like ScannerMaster, The Antenna Farm, Buy Two Way Radios, R&L Electronics, and Zipscanners. Just do some research! I personally use the newly released Wouxun KG-Q10H and a professional Laird EXH160SFU antenna for mobile & field usage and this pairing is exceptionally great. The aforementioned Wouxun was purchased on Buy Two Way Radios, and the Laird antenna was purchased at The Antenna Farm.