The way they think time works is stupid then.
It's sort of a wibbly wobbly ball of stuff.
But I figure the basic principle is that: If an event was witnessed by a time traveller, that time traveller cannot go back and alter or prevent that event.
It's a pretty shaky theory, but it (or something similar) could explain why the Time Lords could bounce around time until they had experienced the bubble.
Or possibly the Doctor simply damage the time vortex enough in that period of time and space that time travel was virtually impossible.
Ok, I give up. It's more fantasy than science fiction.
$̵̵͙͎̹̝̙̼̻̱͖̲̖̜̩̫̩̼̥͓̳̒̀ͨ̌̅ͮ̇̓ͮ̈͌̓̔̐͆ͩ̋͆ͣ́&̾̋͗̏̌̓̍ͥ̉ͧͣͪ̃̓̇̑҉͎̬͞^̸̠̬̙̹̰̬̗̲͈͈̼̯̞̻͎ͭ̐ͦ̋́̆̔̏̽͢$̻̜͕̜̠͔̮͐ͬ̍ͨͩͤͫ͐ͧ̔̆͘͝͞^̄̋̄͗̐ͯͮͨͣ͐͂͑̽ͩ͒̈̚͏̷͏̗͈̣̪͙̳̰͉͉̯̲̘̮̣̘͟ͅ&̐ͪͬ̑̂̀̓͛̈́͌҉҉̶̕͝*̗̩͚͍͇͔̻̬̼̖͖͈͍̝̻̪͙̳̯̌̅̆̌ͥ̊͗͆́̍ͨ̎̊̌͟͡$̶̛̛̙̝̥̳̥̣̥̞̝̱̺͍̭̹̞͔̠̰͇ͪ͋͛̍̊̋͒̓̿ͩͪ̓̓͘^̈ͥͩͭ͆͌ͣ̀̿͌ͫ̈́̍ͨ̇̾̚͏̢̗̼̻̲̱͇͙̝͉͝ͅ$̢̨̪̝̗̰͖̠̜̳̭̀ͥͭͨ̋ͪ̍̈ͮͣ̌^ͦ̏ͬ̋͑̿́ͮ̿ͨ̋̌ͪ̓̋̇͆͟҉̗͍$̛̪̞̤͉̬͙̦̋ͣͬ̒͗̀̍͗̾̽̓̉͌̔͂̇͒̚̕͜^̧͎̖̟̮͚̞̜̮̘͕̹͚̏ͩ͐ͯ͑̍̍̀͒͘*̿ͨ̽̈́͐ͭ̌̈͋̚͟͝҉͕̙*̨̢̭̭̤̺̦̩̫̲͇͕̼̝̯̇ͨ͗̓̃͂ͩ͆͂̅̀̀́̚̚͟%̨͚̙̮̣̭͖͕͙ͣ̽ͮͤ́ͫ̊̊̐̄̌ͣ͌̉̔͊̽̾ͨ^̢̹̭͍̬̖͇̝̝̬̱͈͔̹͉̫̿͛̄̿͊͆ͦ̃ͮͩ͌ͭ̔ͫ̆͞ͅͅ%̵̼̖̻̘ͪͤ̈̃̓̐̑ͩͭ̄̑͊ͫ̆̌̄͡*̴̮̪͕̗̩͇͇ͪ̑̊̈́́̀͞^̼̝̥̦͇̺̘̤̦͕̦̞͑̑ͯ̂ͯ̕͞%ͮͫ̿ͫ̊̈̔̍҉҉̴̸̡*̛̭̖͇͚̝̤̬̰̅̎ͥͯ̓͑̾ͬͨͮ́̕͝^̧̽͋̈ͤͮ̈́́̍ͧ̊҉͇̙̣̯̀́%̴̡̛̘͚͈̗̖̮̫̏̆ͦ̽̔̈̽͒͛̈