It looks like the font sizes were indeed changed in the AZW3 files. Theoretically this shouldn't happen unless you've added an additional CSS file or CSS rules in Calibre. Select Preferences > Common Options > Look & Feel and make sure that no CSS file paths or CSS rules are shown under Extra CSS.
If Extra CSS is empty, try converting your ePubs with
Kindle Previewer/KindleGen, split it with the
Calibre KindleUnpack plugin in Mobi7 and AZW3 components and have a look at the AZW3 file. If the KindleGen generated styles look more or less OK, you may want to ask a moderator to move this whole thread to the
Calibre Conversion forum, because you might have found a rare Calibre bug that only Kovid Goyal can help you with.
EDIT: I converted the original file myself and can confirm that Calibre does indeed change the paragraph font size from 16px in the original file to 20px in the converted AZW3 file. A KindleGen generated AZW3 file doesn't have this issue. There appears to be a bug in the AZW3 converter.