When one has two Clips, that have had their In & Out Points set, and there are sufficient Handles, the Transitions will be applied, as one would anticipate. When there are no Handles, the frames must be duplicated to "create" Handles, or one must Trim the Clips (setting the In & Out Points) to get the Handles.
This graphic will give you an idea. It shows traditional A-B Roll editing so you can see what needs to happen. In the case of most NLE's, the Clips are on the same Video Track, but the Handles still must be present. Look at the "overlap" and imagine this on the same Video Track.
Here is the F1 file page on Handles:
The reason that two of your Clips worked fine, but two did not was that in the first case, you had set the In & Out Points with Handles, where with the other two, there were no Handles - only the Clip ends.