Sorry to hear that. If they are not formed this late in the hatch then the temp is most certainly lower than average. (If you are using a still air bator it should be 101-102 degrees and if you are using a forced air incubator it should be 99.5.) If you have a problem in future hatches getting the humidity up, try using a couple of wet sponges in the bator. I too would leave them in there as long as you see signs of life. If it's smelling in the bator though you need to try to locate which egg it is and get it out of there.
99 is not cold for forced air. It's actually recommended at 99.5. While most hatches have action by day 21 it is not necessarily true that you will. 21 is just an average. The recommended humidity is at least 65% for hatch, but I agree with you on higher. I strive for at least 75%.
Another question would be how is the hatcher counting the eggs? Day one does not start until 24 hours after they are set. You don't count day 1. That can make a big difference as to whether they are "early/late" or "on time". Many people do not realize that you do not count the day you set them and get overly anxious when they feel their eggs are "late".
There's definitely things that need to be tweaked, but don't give up or let it discourage you from trying again. Due to a faulty thermometer my first hatch yielded two that actually hatched way late and only one of the two survived. Next hatch, after I figured out the problem and took the steps to correct it, I had 13 hatchers out of 16 eggs.