What are AC remotes?

Since you aren't using the macros to set the bits in TCCR2B, what bits are you setting in that register?

Why are you setting them AFTER the compare registers?

What was the also sketch that you uploaded and what hardware have you connected to it before?  (Not just what was connected when the problem started)

If loop back is failing and pin 13's LED never blinked, return it.

What do I do?

Install the FTDI drivers from ftdichip.com.

You need to setup a simple state machine or at least use state variables.

Here's a tutorial I wrote on how to use millis (and state variables) to flash LEDs.  The code goes from using delay to using millis.

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

Please post code

Bit 7 of SREG is the global interrupt bit.

The function stores the value of SREG, disables the bit, then returns the bit to its previous state.

I searched the  preferences.txt file for "serial" and only thing I found was:

Okay so ADD the line then.

last.serial.location=51,22,500,500

Could installing HyperTerminal have something to do with it messing up the serial monitor's resize?

Only in the same way that launching Solitaire changes the current font you are using in Word.

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().