Since I have never used iPhoto or Photos (and don't intend to) my ability to help is limited. However a workaround would be to locate the Photos files in the Finder then drag and drop (or import) from there. Information on how to do this is here: http://osxdaily.com/2015/04/22/show-original-file-from-photos-app-mac-finder-osx /
There seems to be an option of either storing the actual photos within a library or only having references in the library to photos stored elsewhere. This may explain the different experiences people are having in accessing their Photos libraries within iMovie.
The symptom of photos appearing black in iMovie under El Capitan is being frequently reported, whichever version of iMovie is being used, which suggests that it is connected with El Capitan and something unusual (and yet to be identified) in the affected person's software configuration.
In such cases it may be worth creating a new login account and seeing if this behaviour in iMovie persists.
Geoff.