I have a couple of places in my mod where I've extended one of my own scripts (created a base class with functions and data common to some task, then created multiple variants of it by extending that same script.) I notice in the first instance that I did this, the source and compiled versions of the parent class were included in the .bsa the CK created when I uploaded to Steam, and that stuff seems to be working fine. I recently did it again though, and the .bsa created does not contain the parent class's compiled or source files, and I've had some reports that that stuff isn't working.

Does anybody know if parent classes must be packaged along with any mod that uses them, and if so, whether there are any circumstances under which the CK will fail to do so when packaging a mod? I took a look at the "Extending Scripts" section of the CK wiki, as well as the "Uploading to Steam" section, and neither one mentions anything about this.

You could check your child pex files with the dis-assembler, a quick peek at the output will tell you if your parent file routines are included in that.
From what your users report I'd guess not. (If you call the assembler without any command line params it will print the usage.)

The BSA http://www.creationkit.com/File_Menu#Create_Archiveis flaky. It says there that you have to pretty much keep your own manifest.