Thanks for the reply.
Your advice on using the ipod helped me determine it's definitely the subwoofer. I connected only the ipod to the sub and after the sub warmed up (maybe 15 minutes) I started hearing the thumping noise.
I did some further testing and here is what I found out.
After the subwoofer has been warmed up, the connection seems to turn off and on. What I mean is, there's a light on the back of the sub. Red means no signal is being sent to it's in a power off state, and green means a signal is being received and the sub is powered up completely. During these "thumping" sounds I hear, that light is turning from green to red and back to green.
Basically... the subwoofer seems to be cycling from a power on to a power off state and then back on again. It doesn't matter if the source is my receiver or my ipod... so it's a problem with the subwoofer. This power cycling appears to only happen once the subwoofer has been warmed up after 15-30 minutes of use.
I'm glad to know where the problem is originating from now... so thank you for the tip to try the ipod. Now I guess it's time to make some calls and see how much this will be to get fixed... or if I should just order a new sub.
Edit: When the light changes from green to red to green, I also hear clicking noises. I mentioned earlier in this thread I sometimes heard clicking... so that's where it's coming from. Hopefully it's something easy and cheap to fix (like a power supply or something (at least I hope that's cheap))