Please see About → System info BaseVersionName and ServerVersionName. I suspect an uninstall does not remove all of the updates (might also be OS-dependent), and if so a leftover update could still be found. There’s a search at Duplicati startup time done by the version you install, and it may run some later update.
Downgrading / reverting to a lower version would be worth reading if you’re trying to revert to an old version.
I don’t have much to say about performance difference between command line and GUI. It does seem odd. Both could probably be improved by choosing sizes such as –blocksize to be larger to help larger backup. Keeping track of lots of little blocks inside lots of somewhat larger remote volumes can make DB get slow.