The "whatever" was supposed to be installed but wasn't error is a cosmetic bug and can be ignored.
When doing a major update to what can be considered a system DLL now such as replacing all the gcc*.dlls or updating libc, you should do a reboot because otherwise the DLLs are unlocked, loaded into memory, and then replaced while the old DLL is still being used by any program that was using them.
The idea of a package manager is good. The problems are, RPM was the first Linux one and being first has weaknesses. And we have a shortage of manpower so there is only 2 or 3 people maintaining all this stuff and they're going to make mistakes as they're human. I've been beating on yum/rpm to test the new graphical front end and I have not been impressed by the underlining RPM.
The other problem is that we're running a hybrid system. Software installed by the system, warpin, yum/rpm, and users just unzipping stuff.
What happens if various GCC*.DLLs or LIBC06*.DLLs are installed in x;\ecs\dll, x:\os2\dll and @UNIXROOT\usr\lib? Depending on your libpath it can be DLL hell. Good idea to watch out for duplicate DLLs and maybe put @UNIXROOT\usr\lib in the front of LIBPATH