Wow, very interesting. I can't do the uninstall right now, but thought I'd run the ngen command (because I've never seen it before.... go figure).
Anyway, interesting output related directly to Paint.net:
Failed to load dependency Microsoft.VisualStudio.OLE.Interop of assembly Microsoft.VisualStudio.Tools.Off
ice.ContainerControl.v10.0, Version=10.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a because of
the following error : The system cannot find the file specified. (Exception from HRESULT: 0x80070002)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency PaintDotNet.SystemLayer.Native.x86 of assembly PaintDotNet.SystemLayer, Version
=4.5.5454.39504, Culture=neutral, PublicKeyToken=null because of the following error : An attempt was mad
e to load a program with an incorrect format. (Exception from HRESULT: 0x8007000B)
Failed to load dependency Microsoft.VisualStudio.OLE.Interop of assembly Microsoft.VisualStudio.Tools.Off
ice.ContainerControl, Version=10.0.0.0, Culture=neutral, PublicKeyToken=b03f5f7f11d50a3a because of the f
ollowing error : The system cannot find the file specified. (Exception from HRESULT: 0x80070002)
My next task would be to DO the uninstall/reinstall, unless you can see something that would suggest another issue.