dashiichi: No specific remedy but some things to try:
Reset the interaction key back to the default for a check. There may be something weird in the API code for that particular interaction which doesn't like the numpad -- even if numpad 5 works on other things.
Change over to using the personal refiner. That takes up one suit slot but, of course, so does the portable refiner when it's not in use. Big advantage is that it can't get lost. One disadvantage is that it can be damaged by, e.g., changing galaxies but it's cheap to repair.
Craft a medium or large refiner at a base or on your freighter, especially for those procedures which take a long time to complete.
I changed the interaction key like you said. It works. Apparently the num 5 key is somehow set to pick it up.
Thanks for your help.