Try trashing your InDesign preferences.
To do so on a PC:
You can try the quick way of resetting on a PC which is to hold down Ctrl + Alt + Shift when launching InDesign and respond affirmatively when asked if you want to reset. There have been some recent reports that the window asking if you want to reset is not popping up but that the prefs are being reset anyway. If this works great but if it doesn’t you may have to manually delete them.
To do so:
On Windows 7 and above the preference files are hidden. To find them go to the Control Panel and open Folder Options and then click the View tab. Then select “Show hidden files and folders” or “Show hidden files, folders or drive options” in Advanced Settings. Then delete (or rename) the folder at the end of this path: C:\Users\<USER>\AppData\Roaming\Adobe\InDesign\<Version #>\<Language>. Make sure that InDesign is closed when you do this. When you relaunch the program it will create new preference files and the program will be at its default settings.
The advantage of manually deleting preference 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.
Thanks for the reply Bill. I tried manually resetting my preferences but I'm still having the same problem. Before you said that I thought it had something to do with preferences because I had recently changed the setting "General > apply scaling to stroke weight" and I noticed that the problem started happening after I made that change.
Update: It's working correctly on other documents but not on the original one. I'll copy everything to a new document.
Glad it's working.
Instead of copying to a new document, save as idml file and load that. On complex files that is faster.
Great! Thank you for everyone's help.