Something like three wrongs led to one right. Core issue (not starting with line 0 but line 1 and not using the current line but the current line from the gcode file being sent, regardless of reset by M110) should now be rooted out.
The location of the config folder has changed. OctoPrint will try to migrate the configuration from its old location (~/.printerwebui, ...) to its new one (~/.octoprint, ...). For this to work the following conditions must be met: 1) the old config folder exists and is a directory 2) the new config folder does not exist at all. The migration functionality will be in the future.
Gina Häußge