No idea what is causing you to lose your Atari 7800 bios image where the base machine doesn't even load.
Loosely loaded Atari 7800 cartridge images require a "header" in the file (header+data=image) - A78 Header Info
A small number of early consoles when emulation was first developed created a header (or some sort of in program detection) to handle images. In the Atari 7800's case for MAME, the softlist contains images ONLY (no headers) and each entry details exactly how to handle mapping and identification and can only be loaded though the internal specifications. Loading externally through the "picker" style of loading using command-line and specifying a location will only work with those files that have a header that information can be detected from (.a78). In short, as soon as you include a media type (-cart) and a literal location (c:\roms....) to load an image not controlled by rompath, it denotes the image as "picker" style loading and, as I mentioned before, for the Atari 7800 this requires a file with a header to be properly loaded and detected.
Assuming you are using the confirmed softlist roms:
> mame a7800 pacman - WORKS
> mame a7800 -cart pacman - WORKS
> mame a7800 -cart c:\roms\7800\pacman.zip (assuming it is from the data only softlist image, without header) - DOESN'T WORK
Hopefully this helps.