I have same issue.
Re-install full 13v5 doesn't resolve.
deployment.log shows everything is 'succeeded', but PHP handler is not there.
12 02, 2014 1:11:53 org.apache.catalina.startup.Catalina initDirs
SEVERE: Cannot find specified temporary folder at ..\temp
It seems repaired.
IIS URL Rewrite Module
Microsoft Application Request Routing
Microsoft External Cache for IIS
Microsoft Web Farm Framework
and reinstall FMS, others are auto-installed.
I'm not sure for this is the key, since too many things I did before resolved... disable IIS, install FMSv3 etc.
I changed install option to unchecking PHP/XML (default) last time, but this shouldn't key. After install, they can be on.
catalina...log is saying same SEVERE error, so this may be not a problem.