I did the same updates on my system which is Windows 7 64 bit, and I installed the .net 4.5.2 and my taskbar settings are staying the same.
When you change the taskbar settings they get saved to the registry. It is possible that it is failing to save those settings and so at next reboot when it goes to read the settings it takes what ever was there before since they didnt get updated.
It is possible that the permissions on that registry key got messed up, or you may just need to delete the key and have windows save it fresh.
Some of the registry settings are store at
HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Policies\Explorer
And the other location, which the toolbars you add to the task bar and such are stored at
HEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Streams\Desktop
I say export both those locations as a backup, and then delete them and reboot. Once back up go and change the settings on the taskbar and se if they save and reboot again to confirm they held.
Shane