We were passing a unicode string to 'runcmd' in the path to the .crt file.
That is because the keyname was coming from ovf file as unicode.
Ie:
u'/var/lib/waagent/6BE7A7C3C8A8F4B123CCA5D0C2F1BE4CA7B63ED7.crt'
Then, logging was extending not appending errors.