Evernote unfortunately has a lot of problems with PDF export (and with printing too!). I have reported several issues, some of them 3 months ago:
#3811711 / Spaces between words with different formattings are disappearing when exporting to pdf
#3817922 / EN 10.72.2 Win - print problems
#3871050 / EN 10.84.3 Windows, task info missing in pdf
#3871010 / EN 10.84.3 Windows, empty lines missing in pdf
#3871017 / EN 10.84.3 Windows, link colors missing in pdf
#3870956 / EN 10.84.3 Windows, divider lines missing in pdf
#3870882 / EN 10.84.3 Windows, table borders missing in pdf