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1. Yes. Anything can happen with a pdf. The results of conversion are usually far from satisfactory unless you are prepared to spend substantial time on editing.
2. There can be many factors that contribute to this. The three formats are very different. In the particular case you describe it may well be because of some peculiarity of the original pdf which does not convert well to mobi.
3. In the top left corner of the conversion screen there is a drop-down menu which lets you select the source format to convert from.
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