This is true, I came over this piece of information myself when I had stood in line to check in at the Kuala Lumpur (KUL) LCCT (Low Cost Carrier Terminal) with the airline Air Asia. If this is restricted to only Air Asia or the same applies to other carriers at the LCCT I am not sure.
I do not remember how much the "fine" was, but it was not dismissively little for us traveling on a budget.
To be fair, you are informed when booking with Air Asia that extra charges might occur during check in when flying through an airport with such a system. However during this leg of the trip I was not the one booking the ticket and had not received that information. This piece of information is easily lost when trying to go through their very complex booking system.
I believe that there are other airports that also have the same warning flag raised when booking through the Air Asia website, but I am not sure. And when I last checked it said something along the lines of "...charges might occur...". As in they don't explicitly say that it will cost extra to not do the online check in, but might.
As far as I can tell it does not matter if it is domestic or international, if you have to check in it applies to you.
EDIT: This was in April of 2012.
EDIT 2: Air Asia provides online check in through website (printer needed I believe), through your phone (smartphone with display to show barcode) and machines at the terminals it flies to. The machines will want the confirmation paper with the barcode that you received in your email. I believe you are able to type in said barcode/booking information in to the machine as well if you don't have it printed.