It could be a ganglion. That is a lump or knot that forms with fluid. I had one for about three months, then it went away for half a year and came back. If that's what it is the doc says they may fill and drain on their own unexpectedly. You can have them drained or surgically removed. Wikipedia gives a better description...Good luck!
Various possibilities are there.It can be a ganglion(a swelling that often appears on or around joints and tendons in the hand or foot) , aneurysm(a localized, blood-filled dilation (balloon-like bulge) of a blood vessel caused by disease or weakening of the vessel wall.) , callus(may cause pain if irritate the nerves) or infection.
Fractures do cause pain but don no cause localized swelling as the one you are describing.Moreover,the x-ray also has come out clean.So it is less likely a diagnosis.
I sincerely advise you to discuss these possibilities with a podiatrist and get your daughter investigated for these.Various investigations are required to rule them out and confirm the diagnosis.
Hope it helps.Take care and pls do keep me posted on how your daughter is doing or if you have any additional doubts.