Can someone give me guidance on how to stop my plug-ins from appearing every time I open an X3 Producer project? I have to spend time minimizing the plug-ins I used in the project (Breverb, Ozone, etc.) before I can get to work. Thanks!

Close the plug-in UIs or dock them.

One project of mine kept doing this. Haven't been able to fix it, guess the project got corrupted. You could try removing the plugins from the bin (saving the important settings if necessary), saving the project, adding them back in and saving again. Use different names for the saves to make sure you don't get a REAL corruption and overwrite the original.

Before saving and leaving the project, click the X in the upper right corner of the plugin box, instead of minimizing them and pressing the -
This works on all my projects. Thousands of them....
CJ

Agreed. Don't minimize them exit them. They still work in the FX bin you just don't have the GUI open.

I'm saying this happened to me, and no matter whether I closed them or not, they popped back open when I opened the project again. I practically always close plugs, and never minimize them consciously. I think it's a variety of project corruption. It was always the same set too, and they opened in a configuration that I had saved a few versions earlier (like, analyzer next to EQ and comp).

Sanderxpander
I'm saying this happened to me, and no matter whether I closed them or not, they popped back open when I opened the project again. I practically always close plugs, and never minimize them consciously. I think it's a variety of project corruption. It was always the same set too, and they opened in a configuration that I had saved a few versions earlier (like, analyzer next to EQ and comp).

I'm sorry but I don't see how that is possible. If you save the project with all your plugins exited i.e. closed that is the way it will open. I don't see how it could do otherwise. You mention corruption but I wonder what sort of corruption could cause that symptom? Activating a GUI of a plugin seems a bit far fetched. 

I could send you the project if you like. Unless you'd like to insist that I'm lying.

I believe you Sanderxpander............ :)
 

I've had this happen with projects before. A totally random plugin (I can't remember which now) that I never really had the UI open for other than when I first set it popped up on project open. 
 
There's also the opposite problem, where certain plugins need to be open in order to properly load (EZ Drummer and Broomstick Bass for example).