We've had many kicks at silent installation of JRE (we're a LanDesk shop), and if it occurs during a user session with an open browser, it can completely mess up the installation. I've submitted a bug report on this already (1669879).
Inside the %PROGRAMFILES%\Java\JRE6\bin folder is the Microsoft Runtime Library file MSVCR71.DLL that gets locked if a browser is open. During installation, the older JRE6 version is removed (unless it was installed with the STATIC switch) except for MSVCR71.DLL. Then the silent installation begins, with the core.zip expanding in alphabetical order until it comes to the letter m where it finds MSVCR71.DLL and just stops (in a non-silent mode, the user would be thrown a dialog to quit the browser / jqs, etc.). No roll back, no repair, etc. So now your left with some residual files, some reg entries but no control panel, no entry in the ADD/Remove Programs list (ARP), no regsvr32 registration has occurred.
MSVCR71.DLL See (MS KB326922) is distributed with an app when the application was developed with Microsoft Visual C++ .NET 2003. This file doesn't change (unless the Visual Studio gets upgraded) as JRE6 updates get incremented. A solution for the developer might be to skip this .dll if it is encountered during expansion of the core.zip file. Or how about an .msp file instead of full blown installers?
Using Group policy in a networked environment to push JRE will work if done correctly (using software installation or computer startup script).