could be anything. I have a pc makes strange morse code beep-like sounds when cpu is in low frequency, like when idle. could be a fan, could be something on mobo. make sure all ur caps are ok on the mobo, (not bent or ready to pop) if so most likely safe to ignore. I've ignored it for 7 years.
In ur case its the extra frequencies needed for graphics and virtualization processing that seem to be causing it which is more common.
What do u mean by qubes is crashing. do u get anerror message?
try diff power settings on the mobo.