If you get not separated biosrom file /missing BIOS rom messages you should investigate the datfile for the mentioned name. Especially if the BIOS entries are well defined in the dat. There was a change in 4.x regarding the option to "keep bios files separated" but actually it was only an alignment of the rebuilder/scanner functions for this.
Default should be "separate bios sets" enabled in scanner advanced and rebuilder advanced.
I took a look at the datfile, and the problems stem from the only two bios entries where a bios is defined as using another bios, and games are using the derivative bios. They both look something like this:
<game name="foo" isbios="yes">
<rom name="baz"/>
</game>
<game name="bar" isbios="yes" romof="foo">
<rom name="baz" merge="baz"/>
</game>
<game name="game" romof="bar">
<rom name="baz" merge="baz"/>
</game>In these cases, clrmamepro 4.01 wants to keep the two bios copies of baz separate with one copy in each of the bios zips, and wants to leave baz out of any games defined as using bar as a bios (given a split-merged set).
On the other hand, the torrent files, which were supposedly successfully scanned with clrmamepro 3.138a, keep only a copy of baz in the foo bios, leaving the bar bios without baz. The games using the bar bios, however, include baz.
Again, I don't have a copy of 3.138a to verify that it does in fact do this, but seemingly knowledgeable people claim that the torrent files scan fine with that version.
All the rest of the games that simply refer to a single bios scan fine.