After the second reboot. both scan engine version entries (32 and 64 bit) now show the 5500 engine.
Oddly mine was the opposite showing the 64bit being correct and 32bit being incorrect. However verifiying the files on the system they both show 5500 as the file version information. The engine updates always seem to be the most picky about getting their data version information showing correctly.
I have done some tests and here are the results:
After the upgrade from ePO on the agent about screen the engine version was still 5400.
After around 1 min the engine for 32bit is 5400 and for 64 bit is 5500. ( win 7 enterprise 64 bit VM 1CPU 2GB ram).
I can see in the registry the engine version for both 32 and 64 bit major and minor is 5500.
After around 5 min in the agent status screen for both 32 and 64 bit changed to 5500
McAfee agent 4.6 P1 with VSE 8.8P1 managed from ePO 4.6P1.
The machine was rebooted and all seems ok for now.
Thanks for the feedback.
This is an issue with VSE and we will inform the same to the product team.
-Mcafee AV Engine Beta Team