I have a really weird issue. I am in the process of deploying Agent 5.0. I have deployed it to about 100 PC's thus far, includes Win7x64, XP, Server 2003 to 2012 R2, all are reporting Agent 5.0 is installed excluding one set of Win7x32 which are in remote locations around Australia.
When I click on the Agent and About it says it has installed 126.96.36.19920 but still list 4.8 in ePO. I have tried manually running the Agent and still no go.
Not sure if this is your problem but agent 5.0.0 does not support agent to server communication over a non-secure SSL port. Basically, if your ePO installation does not have the secure (SSL) port enabled for ASCI, 5.0.0 won't work.
MA 5.0.1 supports non-SSL communication.
I've had exactly the same issues (see my other posts) - in the end I rolled the entire estate back to v4.8.xx.
Had a few chats with the McAfee 2nd/3rd line guys a few months back and it seems to be something related to the datachannel size, but we didnt get any further than that.
There wasn't (and still seemingly isnt) any kind of patch for MA v5 forthcoming, so I just cut my losses and went back to a working 4.8.