arduino forever says "uploading to I/O board..." even after sketch has loaded

I am having a problem where my arduino forever says "uploading to I/O board..." even after it seems to have uploaded the project. I am not sure if this is impacting anything but i was wondering if anyone had any idea what is happening.
I am also haveing a problem where it keeps telling me that "serial port COM 3 is already in use." even though every other project is either stopped or closed. The only way to get around it is to unplug and then re-plug the usb cable from my computer.
I am also have trouble with servo code. Would any of my described problems affect this?
Sorry if my questions are stupid, i am new to this.

thanks,
Lucas

Without seeing a schematic or the code you are using, it is more difficult to give an answer.

How is your Servo powered and how is it hooked up? It doesn't seem related, but it is an interesting place to start.

Another thing to try. If just an Arduino (with nothing else attached) is connected to your PC. Does the same thing happen when you upload the simple Blink sketch? (You might have to upload twice before you can see a difference.)