The apps I'm dropping in are replacing ones that already exist within the system. I have attempted to force stop these apps, however, still no result. My workaround has been to decompile the zip, replace what I'm looking to replace (with the addition of some tweaks) and then recompile the zip again.
Kind of a convoluted way of doing things, but hey, that's what I got.
And fyi, it does take care of the vibe issue.
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For those modifying the ROM zip file before flashing it:
If you use windows, 7zip will allow you to drag and drop into the file at any place in the directory structure. No need to decompress the zip, replace files, and repack it.
Ark, the KDE Linux archive program, will do the same thing, sort of. You need to recreate a dummy directory structure with the file you're trying to replace in it, then drag the Root of that dummy tree to the root of the zip file.