I thought I'd write this report in case it helps somebody. Prior to 3.5.6 I haven't had too many issues with Meridian Flips and when I've tried them in daylight with my gear on 3.5.6 they work fine. However, I've been having intermittent issues with the flip not working (mount doesn't move) or flip happens but then capture doesn't restart and Ekos effectively stalls in Capture and needs manual intervention.
What I've noticed is that this appears correlated to when I have a Polar Alignment issue at the start of the session. So, if I forget to disable MF in the Mount tab at the start of the session I get the "well-known" bug where Polar Alignment and MF interfere with each other. When this happens I stop the Polar Alignment, uncheck MF in the Mount tab and then re-run Polar Alignment (which works fine) then continue with the session including checking MF in the Mount tab. Things work fine but if later-on the mount needs to MF I then get the problem I described at the start. I'm guessing that when the MF was triggered during Polar Alignment some parameters got set that then interfere with the MF later in the session. I have no proof of this and can't see anything in the logs to support this but circumstantially it fits with 1) having the problem in 3.5.6 when the Polar Alignment / MF bug appeared, 2) not happening when I do MFs in daylight (because I don't PA) and not happening when I remember to uncheck MF before I PA.
So, if I forget to uncheck MF in the Mount tab before Polar Aligning and get the PA/MF bug, I finish the PA, then reboot Kstars and Indilib.