I have tried to consolidate all my music files to my Itunes Media folder but it is still missing quite a few files. How can I fix this?

So I just bought a new computer and want to transfer my itunes library over. I went through the organize library option and consolidated the files to the itunes media folder, but when i checked the folder it was missing many files still. I tried to consolidate again and it didn't do anything. How can I fix this?

Just to clarify ... you still have media files that are linked correctly from iTunes (i.e., right-click > Get Info, File tab shows the correct location), but these have not been moved to the "expected" location - assuming your iTunes folder is in the default place - C:\Users\username\Music\iTunes\iTunes Media\Music\artist_name\album_title - correct?
There are a couple of other scenarios in which iTunes may not be able to complete the consolidation process:
Some folders in the iTunes Media hierarchy might be set to read-only - to fix this, right-click on your iTunes Media folder in Windows Explorer and select Properties.  On the General tab there's a check box labeled "Read-only" - click the box so that the flag is unchecked and the box is white.  Click OK, and then OK again when the "Apply changes to this folder, subfolders and files" option selected.
Windows permissions issues are preventing iTunes from moving your media files (there's some anecdotal evidence of a change in this behavior in iTunes 12).  See turingtest2's notes on Repair security permissions for iTunes for Windows for advice on fixing this.
Then try the consolidation process again ... if it still doesn't work as expected we'll need to dive further into details of how your media is currently organized and how the non-moving items appear in iTunes.

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