I've not had this problem here. SEP comes up just fine after the install. We're installing AVAS/MAPI/SMTP/PTP on the clients, AVAS only on the servers. If I recall, NTP requires a reboot; but we haven't used NTP since MR2 MP1 or so. But SEPM isn't reporting any new RU5 clients that need a reboot.
I specifed an "Upgrade" install in the GPO since MR5 can overinstall any prior version.
@DavidB1234
If the "Guide" you're referring to is the 3 Connect articles about installing SEP by GPO that I submitted, understand they are not Symantec documents. I'm just a user like you, who figured it all out the hard way! I'll be glad to help if I can, but they're not official documents and there may be circumstances they don't accomodate that are not present in the systems I support, so I don't know about them.
Or maybe Symantec has added to their skimpy GPO documentation now...haven't looked.
Also, if you specify a Replace install rather than an Upgrade install, GP will remove the old version, reboot, and install the new version. You can leave the old Software Package in Group Policy as long as you like (and you need to, until you no longer have any clients on the old version). Are you saying that's what you did? I have not tried it with RU5, but I've never found it necessary to do a Replace install with RU5.
For more information on Replace vs. Upgrade GPO installs, see
https://www-secure.symantec.com/connect/articles/mp-upgrade-path-compliance-using-group-policy, although--theoretically--an Upgrade installation should suffice for SEP RU5. And it did, here.
I can't swear to this, but I'm pretty sure that on the few machines on which I've installed SEP RU5 interactively I haven't been prompted for a reboot either, and all SEP services were running when I was done. If none of the files that get replaced are locked during Setup, a restart isn't necessary.
Finally, if you did not select either Upgrade or Replace for the previous version, the old version will remain listed in Add or Remove Programs. At least, that's the only circumstance under which I've seen this problem. AFAIK it's cosmetic, but you can clean it up by fixing the GPO and using MSI Cleanup Utility on the affected client.
One way you could work around whatever is going on to force a reboot is to use Group Policy Preferences to run a Scheduled Task one time on Startup that runs the SHUTDOWN /R command. Include that in your SEP GPO. Or do a one-time Scheduled Task that launches the services, if that's all that's required.