Whenever you use while True: (sans break) in turtle code, you're defeating the event hander. You should instead use an ontimer() event to run your code compatibly with the event handler. Below is my rewrite of your code to do this along with some other functional and style tweaks:

from turtle import Turtle, Screen
import random
import time

SIZE = 20

class Square:
    def __init__(self, x, y):
        self.x = x
        self.y = y

    def drawself(self, turtle):
        """ draw a black box at its coordinates, leaving a small gap between cubes """

        turtle.goto(self.x - SIZE // 2 - 1, self.y - SIZE // 2 - 1)

        turtle.begin_fill()
        for _ in range(4):
            turtle.forward(SIZE - SIZE // 10)
            turtle.left(90)
        turtle.end_fill()

class Food:
    def __init__(self, x, y):
        self.x = x
        self.y = y
        self.is_blinking = True

    def changelocation(self):
        # I haven't programmed it to spawn outside the snake's body yet
        self.x = random.randint(0, SIZE) * SIZE - 200
        self.y = random.randint(0, SIZE) * SIZE - 200

    def drawself(self, turtle):
        # similar to the Square drawself, but blinks on and off
        if self.is_blinking:
            turtle.goto(self.x - SIZE // 2 - 1, self.y - SIZE // 2 - 1)
            turtle.begin_fill()
            for _ in range(4):
                turtle.forward(SIZE - SIZE // 10)
                turtle.left(90)
            turtle.end_fill()

    def changestate(self):
        # controls the blinking
        self.is_blinking = not self.is_blinking

class Snake:
    def __init__(self):
        self.headposition = [SIZE, 0]  # keeps track of where it needs to go next
        self.body = [Square(-SIZE, 0), Square(0, 0), Square(SIZE, 0)]  # body is a list of squares
        self.nextX = 1  # tells the snake which way it's going next
        self.nextY = 0
        self.crashed = False  # I'll use this when I get around to collision detection
        self.nextposition = [self.headposition[0] + SIZE * self.nextX, self.headposition[1] + SIZE * self.nextY]
        # prepares the next location to add to the snake

    def moveOneStep(self):
        if Square(self.nextposition[0], self.nextposition[1]) not in self.body: 
            # attempt (unsuccessful) at collision detection
            self.body.append(Square(self.nextposition[0], self.nextposition[1])) 
            # moves the snake head to the next spot, deleting the tail
            del self.body[0]
            self.headposition[0], self.headposition[1] = self.body[-1].x, self.body[-1].y 
            # resets the head and nextposition
            self.nextposition = [self.headposition[0] + SIZE * self.nextX, self.headposition[1] + SIZE * self.nextY]
        else:
            self.crashed = True  # more unsuccessful collision detection

    def moveup(self):  # pretty obvious what these do
        self.nextX, self.nextY = 0, 1

    def moveleft(self):
        self.nextX, self.nextY = -1, 0

    def moveright(self):
        self.nextX, self.nextY = 1, 0

    def movedown(self):
        self.nextX, self.nextY = 0, -1

    def eatFood(self):
        # adds the next spot without deleting the tail, extending the snake by 1
        self.body.append(Square(self.nextposition[0], self.nextposition[1]))
        self.headposition[0], self.headposition[1] = self.body[-1].x, self.body[-1].y
        self.nextposition = [self.headposition[0] + SIZE * self.nextX, self.headposition[1] + SIZE * self.nextY]

    def drawself(self, turtle):  # draws the whole snake when called
        for segment in self.body:
            segment.drawself(turtle)

class Game:
    def __init__(self):
        # game object has a screen, a turtle, a basic snake and a food
        self.screen = Screen()
        self.artist = Turtle(visible=False)
        self.artist.up()
        self.artist.speed("slowest")

        self.snake = Snake()
        self.food = Food(100, 0)
        self.counter = 0  # this will be used later
        self.commandpending = False  # as will this

        self.screen.tracer(0)  # follow it so far?

        self.screen.listen()
        self.screen.onkey(self.snakedown, "Down")
        self.screen.onkey(self.snakeup, "Up")
        self.screen.onkey(self.snakeleft, "Left")
        self.screen.onkey(self.snakeright, "Right")

    def nextFrame(self):
        self.artist.clear()

        if (self.snake.nextposition[0], self.snake.nextposition[1]) == (self.food.x, self.food.y):
            self.snake.eatFood()
            self.food.changelocation()
        else:
            self.snake.moveOneStep()

        if self.counter == 10:
            self.food.changestate()  # makes the food flash slowly
            self.counter = 0
        else:
            self.counter += 1

        self.food.drawself(self.artist)  # show the food and snake
        self.snake.drawself(self.artist)
        self.screen.update()
        self.screen.ontimer(lambda: self.nextFrame(), 100)

    def snakeup(self):
        if not self.commandpending: 
            self.commandpending = True
            self.snake.moveup()
            self.commandpending = False

    def snakedown(self):
        if not self.commandpending:
            self.commandpending = True
            self.snake.movedown()
            self.commandpending = False

    def snakeleft(self):
        if not self.commandpending:
            self.commandpending = True
            self.snake.moveleft()
            self.commandpending = False

    def snakeright(self):
        if not self.commandpending:
            self.commandpending = True
            self.snake.moveright()
            self.commandpending = False

game = Game()

screen = Screen()

screen.ontimer(lambda: game.nextFrame(), 100)

screen.mainloop()

Does this provide the kind of response for which you're looking?

To save yourself pain, just use 32bit python, and 32bit pygame. If you mix 32 and 64 bit, it will not run correctly. That's probably the problem you're having.

Since you have python 3.3, you would use https://bitbucket.org/pygame/pygame/downloads/pygame-1.9.2a0.win32-py3.3.msi

You shouldn't have to edit the registry or your environmentvariables unless something goes wrong.