Well, it's good to verify you're not crazy every so often...and I just have
Ran a "diff -qr" between the two partitions (/tmp/sdb3 is my "pristine" partition, /tmp/sdb4 was captured and restored with wimlib 1.8.2-BETA2)
Here are results from the diff:
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Only in /tmp/sdb3: hiberfil.sys
Only in /tmp/sdb3: pagefile.sys
Files /tmp/sdb3/Program Files/paint.net/Staging/PaintDotNet_x86_1468493438.msi and /tmp/sdb4/Program Files/paint.net/Staging/PaintDotNet_x86_1468493438.msi differ
Only in /tmp/sdb3: System Volume Information
Only in /tmp/sdb3/Windows: CSC
Files /tmp/sdb3/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_GDR.mzz and /tmp/sdb4/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_GDR.mzz differ
Files /tmp/sdb3/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_LDR.mzz and /tmp/sdb4/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_LDR.mzz differ
File /tmp/sdb3/Windows/System32/config/systemprofile/AppData/LocalLow/Microsoft/CryptnetUrlCache/Content/94308059B57B3142E455B38A6EB92015 is a fifo while file /tmp/sdb4/Windows/System32/config/systemprofile/AppData/LocalLow/Microsoft/CryptnetUrlCache/Content/94308059B57B3142E455B38A6EB92015 is a fifo
And here are directory listings for the "Different" files
PaintDotNet_x86_1468493438.msi
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-rwxrwxrwx 2 root root 28012544 Dec 7 2014 /tmp/sdb3/Program Files/paint.net/Staging/PaintDotNet_x86_1468493438.msi
-rwxrwxrwx 2 root root 0 Dec 7 2014 /tmp/sdb4/Program Files/paint.net/Staging/PaintDotNet_x86_1468493438.msi
NetFx_Full_GDR.mzz
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-rwxrwxrwx 2 root root 213393078 Sep 12 2013 /tmp/sdb3/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_GDR.mzz
-rwxrwxrwx 2 root root 0 Sep 12 2013 /tmp/sdb4/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_GDR.mzz
NetFx_Full_LDR.mzz
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-rwxrwxrwx 2 root root 213393078 Sep 11 2013 /tmp/sdb3/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_LDR.mzz
-rwxrwxrwx 2 root root 0 Sep 11 2013 /tmp/sdb4/Windows/Microsoft.NET/Framework/v4.0.30319/SetupCache/v4.5.50938/NetFx_Full_LDR.mzz
94308059B57B3142E455B38A6EB92015
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prwxrwxrwx 2 root root 0 Jul 13 2009 /tmp/sdb3/Windows/System32/config/systemprofile/AppData/LocalLow/Microsoft/CryptnetUrlCache/Content/94308059B57B3142E455B38A6EB92015
prwxrwxrwx 2 root root 0 Jul 13 2009 /tmp/sdb4/Windows/System32/config/systemprofile/AppData/LocalLow/Microsoft/CryptnetUrlCache/Content/94308059B57B3142E455B38A6EB92015
As you can see, for the first three files the size of data is zero in the wimlib restored partition, so something happened when restoring.
Not sure what the issue is on the last one but it's a special file so I'll leave that to the expert (you).
I'll give you any other data you need later but hopefully this is helpful
Thanks for your assistance.