Hi. Just touching on this briefly (search for something different brought me back to it).
By deploy a binary file, or a script - I thought you meant more than just one file. I also assumed the binary package was using a package manager (e.g., RPM, or installp), or, e.g., a gzipped tar file.
Using Systems Life Cycle you can package one or more files - that BigFix manages using prefetch, brings them all to a working directory /var/opt/BES*/somewhere and you specify a command to install everything in that directory (e.g, rpm -i *.rpm; or installp -d . all)
But it could also be: (chmod a+x filename.bin && cp -p filename.bin /var/opt)
I read you solution as meaning “filename.bin” got copied (deployed) with the wrong file mode and you needed/used a fixlet to correct the file mode.