Thunderbird prefers[1] directory-rel for account local paths and only falls back to directory when the relative pref is absent. To add, the generated directory values were home-relative paths while the app expects absolute paths when reading the setting. Instead of fixing these, just drop the redundant settings. [1] https://searchfox.org/comm-central/source/mailnews/base/src/nsMsgIncomingServer.cpp#745