I can reproduce that, on the own-goto branch. I also have a faster-timeout-fixed, that have both been merged into my master, including swapping the :GX90# over to the new lower timeout commands: github.com/james-lan/indi
I'll make a pull request indi main either later today, or next week.
One nice thing is that with this, the startup time seems limited mainly by Kstars/Ekos. As checking most (3,4, X) of them when kstars is up it's 3-7 sec after hitting start in Ekos to everything being good. When it's the first startup that's more like 10-20.
I'm on a current pull as of just a bit ago (10.03k), I don't see the :%BD# causing an issue. What version of OnStepX are you on? (Mind you this is all testing with a Mega not hooked up atm.)