Been having this issue and unable to find a solution. When using the Project Manager to conslidate a project - I've been running into a bug where I'm 'consolidating and copying to a new location' with handles, some of the video will copy over the entire file (i.e. 25 minute clips). Most of the other assets actually transcode into smaller, but every so often it will try to do some of the entire files. Thanks in advance!
Yes, the Project Manager is really rubbish when it comes to consolidating long GOP / Interframe codecs.
However, there is a nifty, and very simple, work-around for this problem - use Render and Replace.
Essentially, what you do is select all the clips on your Timeline, and right-click on any one of them to bring up the menu, and select Render and Replace -
And then set it up -
For some bizarre reason, Render and Replace does not have the same issues with Long-GOP/Interframe codecs, and it will consolidate your media properly. One thing to note though, is that it does not create a new project, like the Project Manager does, so I duplicate my timeline(s), do Render and Replace, and then select the timelines in the Project window and export those timelines as a Premiere Project, so I now have a new project with the consolidated timelines -