Assuming the trolleys are identical except for the paint scheme, off the top of my head I'd say a combination of:
1) mis-match in the motor. These are typically low-cost DC can motors where the torque vs. speed curve varies 10% or more just from variations in assembly, magnet strength, etc.
2) mechanical mis-alignment or imperfections in gearbox/transmission. This can include variations in wheel slippage; wheel slip occurs more often than you'd think. Traction tires can help but introduce another source of variation. As an aside, this is the folly in adding speed-control electronics which regulates motor speed rather than actual track speed.
3) grime build-up in the gearbox/transmission.
