Clicking noise from speakers (not HD)

Someone suggested that it could be a busted port. However, they did not tell me how likely it was that that was the issue, how I could find out, what that exactly meant, or how I could fix it.
Basically, I had my HD replaced a while ago. The computer works fine, in fact, better than before! But this constant, loud clicking noise comes from both the external and internal speakers. Right now I am using these portable speakers which I attached to the headphone jack. But I'd really like to use my Mac speakers.
When there is nothing plugged into the headphone jack. Only the clicking is audible, there is no other sound.
I know there are more knowledgeable people here who can help. All suggestions and advice will be appreciated.
P.S. Restarting to the desktop doesn't help. Also, when I restart, I get a message that looks something like this:
Incompatible device plugged into Mini-Jack. Please remove or make sure speakers are fully inserted.

Well, I bought new speakers. Thanks for nothing!

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