Well yes and no (the codebase originated as VMS-only). The point is that going to Gnu tools helped us solve the problem, it didn't create the problem (as the OP

Well yes and no (the codebase originated as VMS-only). The point is that going to Gnu tools helped us solve the problem, it didn't create the problem (as the OP was implying). And this is the thing - the complaint seems to come down to "ensuring portability is hard in divergent environments" and the answer is "that should not be the sysadmin's problem, that should be upstream's problem". Up to upstream whether they want to deal with the pain up front in the design, or patch it as it comes.