Sometimes I use ctrl-Y to change some connections to the ones with straight angles, because they can make some patches more readable.
Then I move the horizontal part of the connections up and down, I save my whole project, exit, and reopen the project.
The following happens definitely in hidden sub patches: if I want to make some changes to the sub patch, I right-click on the node in the parent patch, but now the horizontal part of all the connections is at its default position again, namely in the middle between the 2 points.
Of course then the readability of my patch is back to zero, and this makes these connections pretty useless (and frustrating).
Sounds familiar to someone?