FBReader does not support PDF, so you should not see PDFs at all in its BOOK+ ebook explorer. As Shaggy says, if you opened a PDF then it will be in its own directory. FBReader won't list the .pdf file, but it will list the directory containing the PDF file (it lists all directories). There is a difference in icons between directories and ebooks.
FBReader's support of CHMs is limited by the fact that it reads the entire ebook into memory on start-up. Many CHMs are too large to fit in memory, so FBReader hangs or exits strangely. One work around is
SWAP on iLiad, which should allow larger CHM ebooks to work.