It's not 100 %
You need a total of 100 skill points in alchemy to be able to make the Philosophers stone, because the difficulty for the Philosophers stone is 100. If you have exactly as much as the minimum, you can create it, but the success rate is as low as it can get. The higher above the difficulty rating your total score is, the better the chances are. With Eliza, Sophitia, Misty Lear and the item that increases alchemy success rates, it is very much possible, but the chance is very low. You'll just have to keep on trying. The success rate is not displayed anywhere, and you need to add together the alchemy skill points of the 3 characters you use, and add 20 more skill points if you have that success-up item (can't remember its name.).