no, the speaker is analog so putting it in backwards yields sound, it's just that any software that playse with the tones of the speaker will not play the tones properly if it is in backwards. single tone beeps will be about the same either way.
that beep is telling you somehting very important. probably a CPU or memory issue. typically the long beep followed by a short beep is the video card, but you definitely have a hardware problem somewhere. i would start by inspecting the cpu and memory.