It sounds like you are being affected by an issue listed in the Known Issues section of Intel XDK v3900 Release Notes:
The Icons and Splash Screens section of the Build Settings on the Projects tab does not work properly in this release on Mac OSX. If you have an existing project that already includes icons and splash screen images, they will be included with your build package, but you will not be able to replace them using the GUI tool. The issue is being researched and will be resolved in a hot-fix.
To work around this issue, you can reference your icons and splash screen images using the intelxdk.config.additions.xml file. See this sample intelxdk.config.additions.xml file, which is part of the "hello cordova" demo app, for additional information and an example of how this is done. You must still locate your icon and splash screen images within the "package-assets" folder, to insure they will be included with your build package when submitting to our on-line build system or to PhoneGap Build and Cordova CLI.
I'm getting the same issue on Linux build of XDK 3900 having just updated and looked at an existing project. The permissions for the files in the package-assets folder all look OK.
"The Intel XDK was unable to load that file"
All the images are still listed in the file intelxdk.config.android.xml and intelxdk.config.ios.xml
Yes, this is a known issue that is being corrected in an upcoming hotfix (among other bug fixes). You can see a workaround here > https://software.intel.com/en-us/xdk/docs/release-notes-information-intel-xdk < in the "Known Issues" section.