Indesign(any version) opens ALL documents asking for 2 specific plugins!

It seems possible that the Macs with the issue may be using a set of InDesign preferences that were kept when the program was updated. Keeping old preferences after an update can often lead to strange performance issues. Try trashing the InDesign preferences on the Macs in question. This will restore the InDesign program on each machine to the program defaults and will hopefully fix the problem.

To trash preferences on a Mac:

The User Library folder in which InDesign’s preferences are stored is hidden by default on most Macintoshes. To access it make sure that InDesign is closed and click on the desktop to launch a Finder Window (Command-N). With this window in column view follow the path User>Home folder (it’s the folder with an icon that looks like a house—it may have the user’s name rather than “Home”) and click on the Home folder. With the Option Key pressed choose Library from the Finder Go Menu. “Library” will now appear within the Home folder. Within the Library folder find the folder called Preferences and within it find the folder called “Adobe InDesign” and the file called “com.adobe.InDesign.plist” and delete both that folder and that file. When InDesign is next launched it will create new preference files and the program will be restored to its defaults. 

The advantage of manually deleting preference in this manner files is that after you’ve reset up the program (make sure that no document window is open) to your liking, you can create copies of your personalized “mint” preference files (make sure that you quit the program before copying them—that finalizes your customization) and use them in the future to replace any corrupt versions you may need to delete.