See the thread
contentLister displays mobipocket file names after opening. I think this is consistent with your description. As tribble says, using the MobiPocket directory should work for BOOKMOBI files. An alternative, suggested in the above thread by HarryT, is simply to rename the file to whatever you want before MobiPocket Reader opens the file (leave the filename extension "as is"). Or you can edit the manifest file after MobiPocket Reader has opened the file and moved it to its own subdirectory.
Note that this undoubtedly a bug. If the ContentLister can use the title BEFORE MobiPocket Reader accesses the file, then it should certainly be able to do so AFTER access too. The manifest file (presumably created by MobiPocket Reader, or its startup script) is inconsistent with ContentLister's default behaviour for the file type.