I had placed a snipe in well before the last few minutes and even at that lower price I may have still have won the auction (my initial bid was 20% more than the final sale price).
Yes I think if you can't make changes that close to the end of the auction - then don't let the system let you make the change. Pretty simple really.
I don't expect AS to be the end all answer to winning auctions - all I expect it to do is bid what I ask it to (ie at least it could have put in my initial bid which may have still won me the auction).
In future, if I am near the computer I won't use AS. Lesson learnt unfortunately!