Re-checking the code, I can see part of the problem.
PHP's built-in zip-file handling fails; so UpdraftPlus re-tries, using the in-PHP-code zip file handler, PclZip. That's this line:
Zip::addFile apparently failed - retrying with PclZip
PclZip is all-or-nothing; you can add a whole directory to the zip, or have it fail. Most likely nothing is logged after that because it times out. (PHP's built-in zip-file handling doesn't have this problem).
So what we want to work out is why we get "Zip::addFile apparently failed". There are two possibilities that trigger that error. I've tweaked the development version so that we can distinguish from the log which one it is - that'll help. Please can you update again to the development version, and the post a new log:
http://updraftplus.com/faqs/devversion - should show as 1.6.26 or later after installation.
Many thanks,
David