naugustin, if Ekos wants to flip, but mount do a mini slew without flipping, reason is that mount and Ekos doesn't agree about where meridian is. To command a meridian flip is nothing but saying to the mount to slew to the very same coordinates it is pointing to; then the mount, that has tracked the same coordinates past the meridian until now, thinks "ok, someone told me to slew to an object ovest of the meridian, so I should point it from east" and slew to it the only way it knows, moving east of the pier. Problem arise when Ekos (or any other software) sends slew command, but the mount thinks the requested coordinates are STILL EAST of the meridian, so it feels itself on the right side.
You can verify this also inside your house, asking KStars to slew your mount to a star near the meridian; then to slew to a star near the meridian, but on the other side: if the mount doesn't move on the other side on the pier, it's because the mount thinks the two stars are on the same side of the meridian, while KStars doens't agree (actually they don't agree where the meridian is).
My GEM45 behaved exactly the same as yours, until I found that time was not in sync between the to: my problem was the DST settings I think you already disabled. But maybe there's something else you're not seeing
Hope this helps-.

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