First off, there is a minimum 2 cents per share commission. So with the commission that 1 cent stock actually is a 3 cent stock.
Second, in order to prevent players from making money just from buying and selling the same stock over and over again, in addition to the commission the base price for a stock that you buy is calculated based on what your transaction will change the price to. That is probably hard to follow so hopefully a theoritical example will help. Say you are buying a stock that is currently priced at $1.00. You submit your order for 100,000 shares. The program calculates that your purchase of 100,000 shares will move the price up by 3 cents. You will therefore actually purchase the stock at $1.03 per share PLUS the commission. In this case the commission is 2 cents per share (the higher of $0.02/share or 1% of the price). So what will show up in your transaction history is that you bought 100,000 shares at $1.03 for $105,000.
Finally there is what the forums call "chuckage". Say you are buying that same $1/share stock but between when you submit your purchase order and it is executied someone else's purchase of 100,000 shares of that stock is executed. Their purchase changes the price and your later by a 1/10th of second purchase now goes thru at the new price. If this other person's purchase moved the price up 3 cents and your purchase moved it up another 2 cents, then you would end up buying 100,000 shares at $1.05 for $107,000.
I hope that makes sense. Ask if you have more questions.