The install should check for the situation where a reboot after uninstall has not been completed, i.e. HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager, PendingFileRenameOperations exists, and rebooting will remove files from an install that is allowed to proceed before a reboot.

Scenario:
Install 6u10,
Run some java processes or verify java installation in IE 7 and Firefox 2 browsers:
Open IE 7 and navigated to java.com's verify Java - displays 1.6.0_10 installed.
Open FireFox 2 and navigated to java.com's verify Java - displays 1.6.0_10 installed.
Leave browsers open.
Uninstall 6u10.
The uninstall's files in use dialog is displayed:
 The following applications should be closed before continuing the
 installation:
 Verify Java Installation - Windows Internet Explorer
 Verify Java Installation - Mozilla Firefox
 [Cancel] [Retry] [Ignore]
After clicking Ignore, the uninstall displays:
 You must restart your system for the configuration
 changes made to Java(TM) 6 Update 10 to take
 effect. Click Yes to restart now or No if you plan to
 restart later.
 [Yes] [No]
Click No.

Close the browsers so that no Java processes are locked.
Reinstall 6u10.

Restart the machine.

The JRE files in PendingFileRenameOperations are deleted. In this case 6 .jar files are deleted during boot:
C:\Program Files\Java\jre6\lib\deploy.jar
C:\Program Files\Java\jre6\lib\javaws.jar
C:\Program Files\Java\jre6\lib\jsse.jar
C:\Program Files\Java\jre6\lib\plugin.jar
C:\Program Files\Java\jre6\lib\rt.jar
C:\Program Files\Java\jre6\lib\ext\dnsns.jar