It sound like the problem is inconsistent numbering of the file names of the tracks on those USB drives. The BDP-1 will play the tracks within a folder in numerical/alphabetical order of the track names, i.e. 01,02,03,04,etc. If there is no zero in front of the track name and there are for example 12 tracks it will play 1,10,11,12,2,3,4,etc. Some of the tracks but not all being identified by CD1 and CD2 would cause the same issue. You can fix it by changing each track filename to start with the numerical order that you want it to play.
Tony