I know this thread is older but I thought I would share my experience with this same problem. We were installing McAfee Agent 5.0.4 and the McAfee icon was not showing up in the System Tray after installation. Things we tried:
What did work for us, with the help of a McAfee Support Case, was to whitelist McTray in our Symantec Endpoint Protection AV (yes we use Symantec for our AV and McAfee for our encryption). After this the icon appeared as expected!
Note: Here is a link to the article provided to us by McAfee Support: McAfee Corporate KB - kb87544
Just to close the loop on this issue. The System Protect being unchecked only worked for 5.0.2.xxx. I am not sure what McAfee had changed in the newer versions but when I first went to 5.0.2 unchecking system protect worked. Then when I went to 5.0.3 I had the same problem again. This time UNCHECKING SYSTEM PROTECT DID NOT WORK, just as tcox8 noted.
Had several calls with McAfee and I had to "convince them" that the behavior had changed, but at that point all they would do is blame other products for the issue.
We narrowed down the problem to SEP pretty quickly by just removing SEP from a test machine. Be aware when testing this as just DISABLING SEP DOES NOT allow the MCTRAY.exe to run. We tried several things in SEP to white list the mctray.exe executable to no avail, one time it would work the next time it would not.
Then one day I searched again on McAfee's site for the issue and found the SEP article KB87544 given by tcox8.
After changing the settings as prescribed the McAfee icon was consistently showing in the system tray.
I wish McAfee would be more receptive to helping in situations like. Issues like this take input from multiple sources to get things working again.