Alright, I've gotten it reliably to not create links under in expanded mode.

If there is a "large" number of thoughts currently on the plex, and add a new link or thought, the plex will do a special animation--- all links will be dropped, and then each thought will be "re-linked" and the thoughts will arrange themselves accordingly. If you create a new link during this animation, PB will NOT create that link. In other words, if I drag in an URL into an expanded plex, grab its parent gate, create a new parent thought and this new parent thought creation process sets off the "drop all displayed links and redraw plex while relinking all thoughts" behavior, and while that process is going on, if I ALSO drag off a new link from the parent gate of the new URL to an existing thought--- that second parent link will not be created. If just DROPPING the dragged URL into the plex causes a "drop all displayed links and redraw plex while relinking all thoughts" refresh event and doing the same example actions as before--- creating a new parent thought, creating a second parent link to a second existing thought--- then the new parent thought would have been created--- but it would not have been linked. If the plex was STILL refreshing itself while making the second parent link to an existing thought as well, then that link would ALSO have not been created. So for big expanded plexes or for fast linking, you can "not" create many links you thought you had.

This is all with using a non-active thought. You don't have to create a new thought to cause this "not linking when it behaves as if it did" behavior, but it certainly happens more often for me following the creation of a new thought.
Thanks for the detailed explanation of the problem. The animation and updating of the expanded view has been completely redone for the 5.1 release so I anticipate that this issue and others (such as colors not being refreshed automatically) will be addressed by that release.

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