Many dlls operate that way. You register or unregister them from the system they are on. Pritner drivers are kind of like that (print to Pdf for example)
I think traditionally they are NOT treated as portable, as ther are SOO many apps out there where you register the dlls.
I personally would consider as portable those apps that work without this process, but where you have the "option" of making context menues work by registering the dlls.
On my personal key, I keep a half-dozen or so DLLs that work with registration, and have set up a batch file with a menu so I can register or unregister them without typing in whole path/dll-names, etc.
Suggestion: run the start.bat/stop.bat sequence through something like Regshot, and see if there is anything that does not get cleaned up after unregistration.