Actually i'm not sure it is a bug. I think it is more of a feature gone wrong. I can quite easily reproduce it at this point because I finally figured out what was going on.
Any time I add a new emulator Launchbox does exactly what you are describing. It automatically fills in command line parameters. The problem is that it is prematurely suggesting an emulator and filling in the command lines for the suggestion before I do anything past hit the add button. For example, I will try to add rom files for Atari 2600 using the rom wizard. I go to tools>import games>from files. Hit next>rom files, browse for any file, add one, hit next, choose platform>Atari 2600, hit next, click add on choose an emulator, and this pops up:
The problem is, if I choose not to use RetroArch, and insert my own emulator settings instead, none of the preconfigured command line options are removed unless I do so manually. While I am extremely grateful to have found Launchbox and intend to buy it on payday, I have to say that in this instance at least it isn't very clear on what your options are. The prepopulated lists do not look editable other than the "default" checkbox, and it is only by sheer luck and frustration that I discovered that you can click inside the columns and edit them manually, removing or deleting as you see fit.
Like I said, problem solved, but it wasn't very intuitive to figure out what was going on or how to resolve it.
A better solution to this would be for Launchbox to ask you if you'd like to have an emulator suggested and preconfigured in this type of circumstance, rather than doing it automatically. Either that or Launchbox removing all those preconfigured command lines if you don't use it's suggested emulator.
As a side note, typing things into the "Default command line Parameters" entry line section does NOT change what is in the list section in any way, nor as you can see in the picture do any of those command line parameters listed show up in the entry box section. The only way to edit or remove them is to click on the entry inside the listbox itself
Edit:
To try to be more clear,choosing a different emulator from the drop down list DOES remove all those preconfigured settings. What doesn't clear them is when you are adding an emulator by hand that is not included in the drop down list. Ie. typing your own information into the dropdown box - like No$GBA. Which is required when adding your own entries, since apparently the named text in the dropdown list is the only .exe that Launchbox will see when you go to add one.
Another solution would be to have the entries in the listbox show up in the default command line parameters input box. Then it would be obvious how to remove it, provided that edits there affected the entries in the listbox.
Again, like I said, i figured it out for myself already. Just trying to provide feedback so someone else doesn't get stuck with the same issue. I find this program both visually appealing and enormously useful, and I'd hate for people who stumbled onto it to be turned off or stop using it over something like this.