It sounds like you have a post-processing script in Isogen that opens the Iso after it is processed.. This is an option you can turn off in Project Administrator under Isogen>post processing.
As for loading multiple AP applications at the same time, I believe this is possible. AutoPLANT loads apps using pre-defines LSP files, ACAD scripts etc. If you customize your AutoPLANT menu, you can tell it to load more than one. I tried the following and it seemed to work:
1. In AutoPLANT, load the AutoCAD CUI editor (type CUI at command line or Workspace>Customize)
2. Under Partial Customization files, expand the AutoPLANT 3D menu and select one of the application buttons
3. In the Properties of the selected Menu button (in my case Equipment), notice the Macro field. This is used to launch the LSPs, scripts etc. You can combine these to force multiple menus. For example, the Equipment macro is ^C^Cat_equip.. You could add, for instance the Raceways macro to it, so that combined they look like this:
^C^Cat_equip ^C^Cat_elect
Make sure you leave a space so it won't laod both. You also have to keep in mind that Component Preferences will still need to be switched to teh active application when multiple applcations are loaded.
Hope this helps!
Jesse