raw2cdng will not convert multiple clips!

[EtienneSurrette]

I have around 120gb of footage to convert (.mlv to cinema DNG) and up until now I have always used the program raw2cdng to convert my footage.  For some reason, when I finished converting all those clips today with raw2cdng, I found that it had somehow fused all of my clips into two folders of DNG files containing only some of the original clips. 

Help, please.