> The cache should get auto-cleared with the current version. Most likely
> auto-update grabbed a previously uploaded version (which I removed after 2
> minutes). Check the checksum of the exe.
>
Checksum is identical. Redownloaded the zip file from your homepage and installed it on top of my previous installation and wiped the cache manually just to be sure. Scanned with the same result: no unneeded files reported. Checked with an old MAME 0.105 profile, which was still there: it reported plenty of non-separated bios roms.

It came to my mind that there might be a difference if you are using the mame.exe to create the rom data vs. using a pre-made dat file. Since I have not compiled my own MAME from the source for a while, I have been using the dats from mamechannel.it until a binary (either MAME32 or plain vanilla MAME) has been available. The latest one might still have been created in the old fashion. Do you do any check on the data provided by dat files in the same way as the output from the exe is checked or is there any difference, e.g. would CMP just rely on the data to be OK?

In case you need to check this, the dat file still contains all the information you would need to check things like cloneof, romof, biosset in order to make the same analysis as you do with the mame.exe output, doesn't it?