The makefile in the patch lacks at least one important define to make bbdmux (and probably the other tools as well) able to handle files larger than 2Gb. The makefile I found a while ago somewhere on the net contains the following CFLAGS (and the binaries then do work with large files): CFLAGS = -s -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
I've added a call to append-lfs-flags to build with largefile support.