It could be something like that, though I don't see how. From what I understand the signal from the KB just triggers an interrupt, it's a binary condition on/off. If the signal was too weak, it just wouldn't trigger the interrupt. This interrupt tells the BIOS (or the advanced OS for Windows & such,) that the user just hit the combo. At this point the KB is "supposed" to be out of the loop, the BIOS takes over, sends the alert which tells any properly programmed TSRs to do their end process cleanup. At this point it executes a jump to FFFF:0000, which initiates the BIOS startup sequence - thus a warm boot (no POST.) The signal on the KB is supposed to be hardwired, as is the interrupt. All you can do is change where the interrupt goes. The BIOS, during it's startup sequence, programs the interrupt to go to it's warm boot sequence (described above.) Later, an advanced OS (like Windows,) can change the interrupt target to whatever it needs (like the security sequence in Windows NT.)
The only thing that is making any sense to me is the CTRL = Function key aspect of my KVM. Maybe it's causing the hardwired signal to pulse or some such. If the MB is sensitive to this, "maybe" it could cause corruption on the interrupt line, or in a register, or something. Basically, when I hit the combo, even for just a second, the motherboard actually gets a series of interrupts all in a row instead of just a single constant signal.
There was something similar to this causing me problems with my A2000. My first KB adapter wouldn't allow me to ROM switch. The ROM switch board I installed in the Amiga uses the reboot signal to switch. By holding down the reboot combo for 2 seconds, it would switch ROMs and signal with a beep. Only, with my first adapter, it would just reboot like I had just tapped the combo instead of holding it down. My new adapter is a little more versatile, and it works just great. If the signal is pulsing, maybe the first adapter just sent the first signal and waited for the rest to clear up before it started converting again, while the second adapter just passes it through as is, or blends the pulsed signal into a constant.