Repro:

1) Import PackageOne.unitypackage
2) Import PackageTwo.unitypackage

Result:
The second package import reports that there's nothing new to import. This is not true:
Package1 contains: Editor/FileNumberOne.cs
Package2 contains: Edtior/FileNumberTwo.cs

Update: This is only reproducible by creating packages from files that have the same GUID. The repro steps below are what needs to be done to reproduce the packages already included with the case.

1) Create a package from a script file
2) Rename the script file and change some of it's content
3) Create a new package from the script file
4) Delete the packages
5) Import package1
6) Import package2

Result: Unity will tell you that it wants to import the file contained in package1 even though you're importing from package2. After import, you will only have one file. It will have the name of the script in package1 and the contents of the file in package2