Is this the right forum?

Flyduino Nanowii board

Which is what?

I did try to download the multiwii ide

Again, what is that?

if (versionMisMatch == 1) {textFont(font15);fill(#000000);text("GUI vs. Arduino: Version or Buffer size mismatch",180,420); return;}

That looks to be code that runs in something other than the standard Arduino IDE.

I did try to follow the instuctions but I'm kind of lost on what I need to do.

What instructions?  Whatever you are doing, it isn't a standard Arduino thing.  You're going to need to explain more about what you are doing, provide links, or go back to the vendor that sells the board you are using for support.

copy com5 fileName.txt
at the DOS prompt (XP pro) and ever since then my serial monitor's screen with not re-size.

That has nothing to do with the Serial monitor.  I suspect this is a coincidence not part of the issue.

the only thing Arduino IDE installs is the com drivers, and I'm not sure I know how to uninstall them

No, the IDE does not install any drivers.  

The drivers are already built into the OS.  For Windows (I don't know what Windoze is, maybe it is some kind of pirated thing?), you are actually giving it a description file that tells the OS the Arduino is a COM port.  They're actually called description files.

Regardless, fiddling with the COM port won't have any effect on the serial monitor's window size.  The serial monitor just talks to the serial port.  Since the window size is saved in the IDE's preferences.txt file, you can go and modify that.

Exit the IDE, search for "last.serial" and set it to something like:  
last.serial.location=0,0,500,500

Save and relaunch the IDE.

You probably want to look at a real-time-clock (RTC) chip.

The ds1307 is popular.  It works fine when powered, but I found them to lose track of time when run on battery backup.

My favorite is the DS3231 because it is very very stable.

Both work with the Arduino Time library, which will keep track of time without a RTC.  It just won't be as accurate and, obviously, not remember what time it is when the board is reset (or power cycled.)

Did you try the trick mentioned in the comments on http://arduino.cc/en/Main/ArduinoWiFiShield:

"If Arduino Wi-Fi shield is not detected, please make jumper between pins 7 and 3. Then your Arduino will recognize Wi-Fi shield."

That doesn't sound normal.  Please post your code.

What about simplifying the code down to:

Code:

void setup() {
 analogWrite(3, 0);
}

void loop() {
}

Then move the write to loop().  

How are you certain the behavior you are seeing is when analogWrite() is actually writing a 0?

Maybe the A/D on your Micro is working slightly different than your Uno, causing something other than 0 to be written.

I would suggest you include some kind of debug, a LED, toggle an output (watching with another channel on the scope), or Serial.print(), when the analogRead() returns 0 or analogWrite() is called with a 0.  That way you can verify if the behavior you are describing is what is actually happening.

The behavior you are describing shouldn't be happening.  When 0 and 255 are passed to analogWrite(), it turns off PWM and calls digitalWrite() with LOW and HIGH, respectively.

The code portion is working fine, so I don't see a need to post it up.

Post your code.

Thanks for all the help! I connected all the grounds together and everything is working well. I would love to learn what a ground loop is though.

Take what JimboZA said about potential difference between two points and what pwillard said about references, combine them.

Ground isn't special, it's just a reference.  Different points in a circuit that are tied to ground may have slightly different voltage potentials.  This creates a loop.

Read more at:
http://en.wikipedia.org/wiki/Ground_loop_(electricity)

Okay, I will. However, do you know where it might be located? because if it is on the underside I have no way to get to it since my nano is directly soldered in place.

As I recall, it's on the bottom. next to the tantalum caps (yellow parts).

but i whant an delay on the thermostat so it isent changing every milli second but if i make a delay i also get a delay on my servo how do i make a a delay only for the thermostate

Here's how I walk people through using delay() to using millis() to create a state machine.

http://www.cmiyc.com/blog/2011/01/06/millis-tutorial/

Shouldn't the resistors I have drop the current enough to prevent that kind of damage?

No, I didn't see the resistors.  my bad.

I'd still check to see if the diode is damaged, that's the gate between the regulator/5V pin and Vusb.

Showed my teacher. He had no idea what was going on. Guess it isn't working perfectly normally .

Sadly, teachers do not always know everything.

There is a diode between Vusb and 5V.

http://arduino.cc/en/uploads/Main/ArduinoNano30Schematic.pdf

I don't know what that IC does, but if it doesn't limit the current to those LEDs (I'm betting on, it doesn't) then you may have drawn enough current to damage that diode.

While connected to USB, I would measure the voltage across both sides of the diode.

Hardware serial pins aren't broken out.  So as the reference page says, you have to use the SoftwareSerial library to communicate on any of the digital pins.