Hi FreyrGauti,
Based on your description, when the user open documents he got the error message >>The operating system is not presently configured to run this application.<<
Which version of Office are you using? 64bit or 32bit? And which version of Windows System are you using? 64bit or 32bit?
First I suggest you try these methods:
Method 1: Check if Office applications are running in compatibility mode.
Browse to the location mentioned below:
Windows 32bit
C:\Program Files\Microsoft Office 15\Office 15
C:\Program Files\Microsoft Office 15\root\Office 15
Windows 64bit:
C:\Program Files(x86)\Microsoft Office 15\Office 15
C:\Program Files(x86)\Microsoft Office 15\root\Office 15
Right click on EXCEL.EXE< Properties< Compatibility
Uncheck the box Run this Program in Compatibility Mode, Make sure you also click on the option change settings for all users tab at the bottom of the same screen
Click on Apply and Ok.
Open Excel and check if it works.
Method 2: Open Office applications in safe mode to check if the issue is caused by add-ins.
Refer to the link mentioned which explains how to open Office applications in safe mode. If Office applications work fine in safe mode then follow the complete article to disable the add-ins.
After trying these methods, if your issue still exits please try to repair you Office.
About how to repair Office please refer to this link:
https://support.office.com/en-NZ/Article/Repair-an-Office-application-7821d4b6-7c1d-4205-aa0e-a6b40c5bb88b
Hope it's helpful.
Regards,
Emi Zhang
TechNet Community Su