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Mine are all .mp3 file names. Mine are in sdcard/media/audio/ringtones.
Do you think that makes a difference?
What is the format of the custom ringtones? and what is your directory structure on the SD card?
For ringtones / notification / alarms (custom) I use all .ogg files; if you use .mp3, it will work but then they also get tagged in the music player. You can use an online tool to convert files if you need to.
Also, the directory structure I use is below.
/sdcard/Media/Alarms
/sdcard/Media/Notifications
/sdcard/Media/Ringtones
Sorry, I can't seem to replicate your issue..