I've had the same problem as of yesterday. I have the latest patch (non-beta/pre-view) and quite a bit of mods. I found out that when I used the stock 2.5 meter fairing that this happened. Once I removed the fairing everything works as it used to, and should.
Might be my bug is a version and that there are several things causing this, but in my case it sure is the stock 2.5 meter fairing.
*edit*
I found that if I jettison the shroud by using staging (as in hitting the space bar) the problem goes away. Right-clicking on the shroud and jettisoning it means this cloning occurs. It is however possible to first right-click and then have it think it is jettisoning the shroud in the staging queue. I usually end up doing this because... I dunno, I just prefer right-clicking on it...
*end edit*
Fly Safe,
/Akely
