comments/questions?
I think Cubase and the plug-in are simply operating in the 32-bit realm. I suspect Cubase is like CEP/AA in that it does not have a native 24-bit file format. Rather, it opens 24-bit files in a 32-bit float workspace. If one saves the file with default settings, it saves as 32-bit float, even if it includes only 24-bits of audio. In such a case, there are, in fact, 8 extra bits of information in this case - but it just so happens all the information = padded zeroes, i.e. no meaningful content. CEP/AA will only output the actual 24-bits of audio content if one specifies the proper Save As settings before saving the file. I think the plug-in cannot distinguish between the 24-bits of actual audio content and the 8 extra bits of filler, so it reads the file as 32-bit.
Then why don't your 24-bit FLAC-sourced files also read as 32-bit? I'm betting because you simply opened these files in Cubase, but did not then save them in the 32-bit float workspace as you do your FA-101 sourced files.
Wanna test this? Open the 24-bit FLAC-sourced files in Cubase and use the same Save As options with those files as you do for your files recorded from the FA-101. 32-bit files. I bet the FLAC-sourced files then, too, appear as 32-bit files to the plug-in (even though they're 24-bits of audio + 8-bits of filler).