A strange one this. I don't see how changing an LED can have this sort of effect, particularly when the current involved is very small. My current case has an orange HDD LED and my previous one had a blue one, and the motherboards (admittedly different ones) were able to drive them with no problems. You could try putting the red one back to see if that makes any difference. Have you got the leads in the correct place on the motherboard connector, and have you made sure that there is no way for unintentional shortcuts.
When you say freezing, do you mean that the cursor stops on the screen and that you can't move it or get a response from the keyboard? That sometimes happens to me when I try overclocking my graphics cards and take it a bit too far. Are you overclocking? If so, return to stock speeds and see if the problem persists.