Hi,
First, I suggest you try to open these program in Safe Mode. Then check the problem again.
In case this problem disappears, I recommend you may perform a Clean Boot in order to get rid of any other third party software effect.
http://support.microsoft.com/kb/929135
Note: Clean Boot is a step of troubleshooting, we can go back to normal by running MSCONIFG.
If the problem occurs again, please try to run “sfc /scannow” to check system file. Run command prompt as administrator, then type “sfc /scannow” in prompt Windows, press Enter.
Also I am just wondering what you mean “missing”. Could you not find these files in original directory? Please try to list the name of these program which files missing in order to narrow down this issue.
If you have any progress or further question about this problem, please feel free and let me know.
Hope that helps
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