I managed to fix this myself.
I'm not sure that my original question was clear enough to invite a response. Therefore I'll describe the issue more clearly and describe how I solved it.
I'm using Bigbox in a cabinet and wanted to map the LCtrl key to select games in Bigbox so I went to Options > Keyboard Mappings > Select & pressed LCtrl.
The problem was that this added the new key (D1, Return) but didn't delete the old mapping. I then selected Select again, waited 5 seconds to clear and this took me back to the Keyboard Mappings menu, but I was unable to select the Select option again because the key mapping had gone (presumably because I was using the keyboard that I was mapping)
To fix this I opened Launchbox/data/BigBoxSettings.xml in notepad and changed <KeyboardSelect>0</KeyboardSelect> to another code I thought might work <KeyboardSelect>68</KeyboardSelect> and saved it. This maps to Y on the keyboard.
Then I was able to go to Keyboard Mappings, highlight Select, press key Y (the newly mapped key) and then press LCtrl before the 5 seconds was up. It shows two keyboard mappings for Select now but I can live with that. I could always edit the xml file again to remove it.
Is there another way editing the keyboard mappings within BigBox to delete an old mapping and create a new one using the keyboard or is this a bug?