We got this before, I remember in the ambisonic thread or the splitted thread
Since there was a 2GB barrier I decided to split the source 32/44.1 or 48 WAV (at about 40~50 min) in to two parts.
then run besweet transcoding to DTS/DTSWAV
then merge those two DTS/DTSWAV with DTSTrim
finally use besplitt (inoffical beta -special-0.9b7) to fix the file
-> perfect result, needs really less time as merging the single monofiles before encoding into DTS/AC3
maybe you should try this