If a switched mode supply is making a sound you can hear, then there's some component of the switching waveform that's within the audible range. Since 250kHz is nowhere near that range, chances are your power supply is unstable and is switching in bursts, rather than producing a nice, consistent stream of pulses in which every cycle is the same.
This behaviour is generally caused by one of two things: noise, or the wrong compensation network. If the layout is poor, then the controller's sense input gets a noisy signal, and pulse widths will vary quite randomly from one cycle to the next. Or, if it's poorly compensated, then the system will tend to oscillate - pulses will get wider and then narrower, often to the point of being skipped entirely, over and over again.
A scope will show you very clearly which is the case. If your controller has an accessible compensation point (the output of the error amplifier), probe that too as it can give a better indication of whether the problem is noise or oscillation. If it looks like a sine wave, your control loop is unstable and the compensation network needs changing. If it's reasonably flat but noisy, then you need to look at your layout.