I have just encountered this issue too, at the Beta 6 version. It's stopping my scouts in their exploration as they are unable now to fly through the gates/accelerators.
In my case, when I send him to explore a gate/accelerator to unknown sector, instead of flying through it the ship gets a magical order to explore the same sector where it is instead.
To reproduce the issue.:
1. Get some scout ships.
2. Find a jumpgate/accelerator (superhighway will probably have the issue too) to an unknown sector.
3. Select one of the scout ships, right click the jumpgate/accelerator and select the "explore" order.
4. Notice how the ship refuses to acknowledge the order and instead decides to explore the sector where it is.
I am attaching my save. In case of the save, there are two scouts, who are now waiting for further orders - Litigious Rodent and Perseus Sentinel (both are unassigned to). Litigious Rodent is already positioned at an accelerator at Tharka's Ravine XVI sector. Try sending the ship to "explore" the accelerator only to find out that it refuses to fly through it. Also I don't know if it's intended behavior or not but when I order it to "fly to the position" while right clicking the accelerator, the ship flies next to it, but then instead of finishing the order and moving on to the default one ("hold position" in my case), it instead keeps the flying order in the order list, while telling me that it's awaiting next orders.
The second one, Perseus Sentinel, is also awaiting at sector Ianamus Zura VII, where is a jumpgate, which again it refuses to fly the same way as the previous one.
The save is at the link.:
https://www.dropbox.com/s/zlcpwcwt4du7b ... ml.gz?dl=0
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