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The problem has to do with how Google's automated procedure creates epub files.
The cover (as specified in the <guide> section of the OPF) and the beginning of the text are contained in the same file. Calibre removes the cover file and relocates it during the conversion process for compatibility purposes. So all the text following the cover in that file disappears.
The proper way to deal with this would be to separate the cover into its own file and change the OPF accordingly.
If you don't know how to do that, then a quick and dirty alternative would be to remove the <guide> section in the OPF altogether. It presently only contains the "cover" pointer. This creates an improper file but it'll work for your purposes.
From Calibre, right click on the title, select "Tweak Book," then "Explode Book."
Navigate to the OPF file and open it with a text editor like Notepad++.
Delete everything from <guide> to </guide>. Save and close the file and the window displaying the files.
Click on "Rebuild" and then convert this new epub to mobi or any other format.
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