Originally Posted by Clough
Check ceiling underneath toilet for leaks if you have not already done so. If there are no signs of leaks anywhere after a few days, i.e. around the toilet or in the ceiling downstairs, you should be fine.
However, (and this is a hassle) to be absolutely sure you might want to take the toilet off again and put it back on again to inspect it for cracks and make sure that there was not any type of debris under the toilet that could have caused the cracking sounds.
I hope this helps.