.NET 3.5 has become corrupted

Can't fix .NET Framework 3.5 after it became corrupted.
The issue is with the .Net Framework 3.5 which became corrupt when a version of IBM’s client access Vr71 was installed.  We are not able to repair it through any method.
My only win was when I disabled .NET Framework 3.5.1 through Windows Features “Turn Windows Features on or off”. By disabling and then enabling it fixed the issue.
But it only worked on 1 computer. When it doesn’t work we get an error message reading “Some features were not modified. Restart now or later”. No change is evident.
I tried this method: N:\dotnetframework\dotnetfx.exe /t:c:\temp /c:"msiexec.exe /i c:\temp\netfx.msi REINSTALL=ALL ReinstallMODE=vomus"
Thought it was going to work but all populated files would disappear and I couldn’t see any changes. Again, no methods have worked that I’ve tried.
I saw online where a guy used his Windows 7 repair cd to fix the issue so we’ll be going around this morning to each computer and repairing the file structure. If any suggestions can be given, don’t hesitate to let us know. We’ll test them out and get back to you and then continue on with the W7 repair CD.