Your CHARMM versions probably have been compiled with different settings for little_endian vs big_endian representation of binary data in unformatted files; for c32b1 on gnu/linux systems the default is big_endian with the intel and pgi compilers. It is easy to modify to get the native format /little_endian/ to be used instead.
If your system uses the intel compiler this behavior can be changed at runtime without reinstallation; you can also convert the files you already have. Search the forums, or look at some recent posts on format of dcd files.

Lennart Nilsson
Karolinska Institutet
Stockholm, Sweden