At least in some cases, applications referenced with in implicit extension (such as .exe) are flagged as missing by the registry issue scan.
I noticed this with the Sony Ericsson SDK installation:
The Application referenced at "MidletApplicationDescriptor\shell\Install on device" could not be located. These references are often left behind after uninstalling software. Solution: Delete the registry value.
The command value is of the form:
"C:\jdk1.6\bin\javaw" "-Djava.class.path=..." "-Dsdkhome=..." com.sonyericsson.sdkme.tools.Ejava install "%1"
If I add the .exe extension then it passes CCleaner's inspection:
"C:\jdk1.6\bin\javaw.exe" "-Djava.class.path=..." "-Dsdkhome=..." com.sonyericsson.sdkme.tools.Ejava install "%1"