Yes that was indeed my concern - although it's been a while since I've done it because I wasn't sure of exactly what I was "holding". I made a booking, held it and when I went back to buy it, it had gone up by what seemed more than just a change in taxes or additional charges. It's quite possible that they did indeed change but I recall it being a larger than expected amount so I was curious whether perhaps the fare had changed as well in the intervening period.
Now I don't hold things, when I find the fares I want I buy the ticket and if the website crashes when I try and pay for it (which it frequently does) I print it out and email it to the MPC who ticket it at the price quoted on the website.