This is by far the most frustrating bug I found in INDIlib. It's such a headache when trying to use INDI headlessly (only joystick and RPi, phone app eventually)... Reconfiguring over and over, spending valuable time and need for external PC makes me question if this worth, epsecially because I switched from ASCOM because I don't want/have AC plugs to power windows machines on remote sites, besides this I like to use it over WiFi.
So, recently I decided to go down the rabbit hole with it, and found that in my case indiwebmanager cause it (it don't load appropriate configuration, had some permission problems, couldn't run as normal user, as root user couldn't load configuration and thus starts with /usr/share/indi). After few hours of debugging, I figured there is some problem with FIFO buffer I couldn't fix, so I gave up and deleted indi web manager, and INDI finally started to work normally for a while, until yesterday to be specific, which brings me up here again looking for answers...
9 months later I still have this problem. I don't use Ekos. Only indi and indiwebmanager and connecting remotley from windows machine running phd2 or android phone... Not even port settings is saved which I set to static using udev rule (/dev/EQMOD) so auto-connect can't work either...