Opening IntelliJ always wants to clear the readable flag on one of my .iml files

I've got a Flex project file (let's call it main.iml) whose IML file defines a few Flex applications and contains several other modules.  Most of those modules are for SWC libraries.  However, one of them, let's call it other_app_module.iml, is for a semi-related application with its own SWF file.  As such, it is listed in the modules.xml file but none of the applications in main.xml depends on it.

Whenever I open main.iml, I get the following popup:

2014-07-03 15_56_46-Clipboard.png

(the obfuscated part is, of course, other_app_module.iml)

What's going on here, and how can I stop it?

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I have a bit more information about this.  The reason it wants to clear the readable flag is that it wants to muck with $MODULE_DIR$ in the "compiler.theme" entry under <compiler-options>.  My entry looks like this:

<entry key="compiler.theme" value="${FLEX_SDK}/frameworks/themes/Halo/halo.swc&#10;${FLEX_SDK}/frameworks/projects/datavisualization/data_management.css&#10;$MODULE_DIR$/../../shared/shared_lib1/defaults.css&#10;$MODULE_DIR$/../../shared/shared_lib2/defaults.css" />

The directory structure looks like this:

/path
     /to
          /applications
               /special_apps
                                        /main
                         main.iml
               /other_app_module
                    other_app_module.iml
          /shared
               /shared_lib1
               /shared_lib2


As I noted in the first post, main.iml contains/references other_app_module.iml

When I open other_app_module.iml directly in IntelliJ, everything is fine.  But when I open main.iml, it wants to change $MODULE_DIR$/../../shared/shared_lib1/defaults.css to /path/to/shared/shared_lib1/defaults.css (and the equivalent for the shared_lib2 reference.  It shouldn't need to - $MODULE_DIR$ should refer to /path/to/applications/other_app_module no matter where the other_app_module.iml file is included, and so the relative path is correct whether it's opened directly or as part of main.iml.  And yet this is happening.

Even weirder, it doesn't happen to all developers.  The guy who sits next to me opened main.iml, and didn't get the "I want to mark this readonly" message, and IntelliJ didn't try to change his $MODULE_DIR$ reference.  I compared our iml files, our .idea directories, and even tried comparing our settings, and didn't see anything that would account for this.

Can anyone help?

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