I can think of two possible issues, neither of which is a bug.
Please make sure that you are taking a backup with a version of Akeeba Backup newer than 5.5.0. The log path is something determined by ANGIE. ANGIE is included in your backup archive at backup time.
Please also note that the location of the log folder also depends on the Joomla! version detected by ANGIE. The detection depends on some external factors (whether ANGIE can "see" the existence of some files). If the detected Joomla! version does not match you will notice no problem other than this setting reverting to the one used before Joomla! 3.6 (the log folder in the site's root).
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!