Yeah, mame is a little picky about remaps to devices it can't see (such as the unplugged xbox controller). It does sound like xpadder isn't an issue, so mutliplekeyboard doesn't matter.
If you're not using xarcade ctrlr file, but remapped as a normal remap, it's really easy: copy cfg/default.cfg into the ctrlr folder, and point mame's ctrlr option to "default".
The wiki goes into this situation a lot more in depth, including game specific remaps (assuming the reader is starting from scratch). You can copy game specific cfg files into ctrlr file, but it's cleaner to do it the way described (if you want to was game cfgs, let me know and I'll get some hints, too).
If you're using the xarcade ctrlr file, I suggest editing it, adding in the xbox remapped inputs. It can get a little, umm, interesting depending on if you remmapped for lots of games, vs only remapped for all games ("Input (general)"). If you remapped only in the general, you can open cfg/default.cfg and ctrlr/xarcade.cfg in a text editor, and copy all the stuff in default.cfg into xarcade.cfg default system section. You want to leave the inputs that are in xarcade.cfg but are not in default.cfg, and replace the ones that are in both, and add the ones that are only in default.cfg. Save the resulting file as triplex.cfg or whatever you want, and change mame.ini to point to the new ctrlr file instead of xarcade. (Or just save as xacade.cfg and leave mame.ini the same, but you might want to be able to go back to the original.)
Another way to prevent mame from erasing your remaps is a little "dirtier": make default.cfg (and if remapped specific games cfg files) read-only. However, this prevents saving further remaps (and for read-only games cfg files, mame can't save the other info some games it saves in the cfg file). (If the folder was made read-only, then new game cfg files couldn't be created, so those games would always have the OK screen.)
And of course there's the backup, or make copies of, the cfg files, and restore as needed solution, but this can be a PITA to do if you have to do it often. I
really like the ctrlr file option: once done, no need to do anything else.