As far as I remember these things, voltage will regulate the power output of the laser, whereas gain will regulate the sensitivity of the photomultiplier detector. Increase the first and you'll excite the sample more and generate more fluorescence, but if you go too far you'll fry your sample. Increase the gain and your detection threshold will go down, i.e. the signal will look brighter, but so will the background.
Getting the setting right is the case of balancing both settings so that you have a good and reliably detectable signal, your sample is not affected tot he point of changing the result and the background is still low enough not to obscure the reading.
Frying a sample with a flow cytometer's laser, that's a new one... With a normal-spec Gallios, no such thing can happen. Which doesn't mean that high laser power cannot have a negative impact on your results.
The "voltage" is the pre-amplifier gain, i.e. it dictates how much the dectector amplifies the light signal by applying a higher or lower voltage to said detector. The "gain" is the amplifier gain. I believe in BC instruments, you use the gain the adjust the signal from photodiodes, and voltage for PMT's. Check with your application specialist on how to properly adjust these settings.
You can download Howard Shapiro's Practical Flow Cytometry from Beckman Coulter's website for free. Highly recommended if you want to learn the ins and outs of flow, e.g. the collection and amplification of light signals.