Toward the end of my use of the BS2, I just copied files to the SD card, and didn't bother with any of the B&O software because (IIRC), it wasn't updated so it didn't work with newer versions of iOS/iTunes/Windows.
I do recall that there is a specific structure required for the BS2 to find/play songs. It's been many years, but I think there can only be one level of folders. That is, at the top level, you have folders and then within the folders you have your mp3s. I think there were also issues with extended characters in the folder/file names (i.e. those "strange" characters Europeans (squiggles/dots above/below "regular" characters) use in their "strange" (non-English) written languages (I'm joking, I'm joking 🙂 ). You need to stick to the basic ASCII character set.
If this doesn't help, you might try searching the archived forum. I recall there being many discussions over the years about issues where the BS2 had difficulties seeing the files (mostly because of strange characters or nested folders). The solid red on the base means it's fully charged, but not speaking to the computer. Green means good. Flashing means charging/solid means charged. I don't believe red has anything to do with the BS2 actual operation, only it's ability to speak to the computer. The beeps are the BS2 playing feedback, but I don't remember the various beeps mean. Again, the archive forum, or possible the user manual section might shed some light on this as well.