Most plausible explanation, as so often has been the case, is that your have a 32 bit process on a 64 bit machine. In that case the file system redirector means that 32 bit processes that access System32 get redirected to the 32 bit system directory, SysWOW64. That's where you should put the files, if indeed the system directory is where they need to go.
Another possible failure mode could be that you have 64 bit DLLs and a 32 bit process. Or vice cersa.
That said, the system directory is for, well, system files. And applications should not modify it. So, putting the DLLs in the application directory would seem to be the right thing to do. You tried that without success. Hard to say why it failed. Perhaps there are further dependencies. Debug this using Dependency Walker in Profile mode.