I use
4.1.0.1623 and have the same problem.
I put in a new CD, after ripping I see 2 entries but I have only 1 File.
Sometimes the entry is a 8.3 name, sometime it is "*.
mp3" and "*.
MP3".
edit 2013-02-12:
Today I deleted the data base (archive) complete.
After the rebuild - no problems!
Also the ripping of new CD's is OK.
All are OK now. 
I use [b]4.1.0.1623[/b] and have the same problem.
I put in a new CD, after ripping I see 2 entries but I have only 1 File.
Sometimes the entry is a 8.3 name, sometime it is "*.[b]mp3[/b]" and "*.[b]MP3[/b]".
[u][b]edit 2013-02-12:[/b][/u]
Today I deleted the data base (archive) complete.
After the rebuild - no problems!
Also the ripping of new CD's is OK.
[color=#FF0000]All are OK now.[/color] :D