Hey.
I solved this for 5.5 a year ago or so. When you install PowerCLI manually, the .msi-files will be extracted to %temp%.
First up during install of VMware-PowerCLI-6.0.0-3205540.exe is the Remote Console Web Plugin. Look in your %temp% folder while installing. A new folder will be created containing the following file:
VMwareRemoteConsoleWebPlugIn.msi
After this has been installed, PowerCLI is next. Again, a new folder will be created in %temp% with an extracted .msi file for PowerCLI:
VMware vSphere PowerCLI.msi
Try using these files for silent installs, e.g.
msiexec /i "VMwareRemoteConsoleWebPlugIn.msi"
msiexec /i "VMware vSphere PowerCLI.msi"
Try it with the /q or /qn flags if it doesn't work like you want it to.