Unable to shutdown after updates

Hi, at the weekend I had 26 windows updates to apply, they did not install correctly and the computer would not shutdown. After many hours of waiting I forced a shutdown by holding the power off button. I restarted in safe mode and shut down correctly. I had problems restarting so I had a tip about deleting the contents of folder c:\windows\softwaredistribution\downloads after taking a copy of them. I also turned windows update to Never download updates. The machine then appears to start and shutdown ok but at times seems to run slower. I tried a restore to an earlier date but that didn't change anything, and I even re loaded a system image backup that I had taken a few days earlier, interestingly it did not put anything in the windows\softwaredistribution\download folder. I have followed the thread on this forum for update problems which first of all advised me to run the System Update readiness tool, and this installed Hotfix KB947821 ok.
I also ran sfc scan ok. I did another shutdown/restart ok, and then went to the windows update panel and ran Download updates, 28 updates were downloaded, so I unmarked all and then just marked one to install, but as soon as I clicked install it returned to the install button button within 2 seconds. I decided to shutdown and restart, but as soon as I clicked on shutdown the shutdown button disappears and the desktop just sits there with no system activity taking place. I am then also unable to start any other programme, so it looks like I am going to do another forced shutdown. Any ideas on what might be happening and how I can get out of it please.

Hello Archer, thank you for your reply, but before I had seen it I force closed the machine and restarted in safe mode, closed and re started normally Then I checked for updates again and there were 28 updates waiting. I selected just one (KB915597) and installed it ok, then I selected KB2847311 and that one also installed correctly including the restart. I then shutdown and restarted again and all appeared to be ok until I tried to do
something and realised that the system busy symbol (O rotating with arrows) was turning all the time if I put the cursor in the bottom task bar.
I then read your update and am proceeding with the test, but I have one query as I seem to be getting variable results, do I need to start each msconfig test from a boot in safe mode ? ie force a shutdown and reboot in safe mode

Sorry it has taken quite a time to go through all the services and the startup and I am wondering if all these startup and shutdowns may have fixed the problem. After I had finished the msconfig process I have started to re-install some of the 28 updates that I had waiting, so far I have installed 17 of the updates in small groups and everything appears to be working correctly again. I will let you know later when they are all installed. Thank you for your help with this. One other question, I notice during the startup that I get a message on my desk top for a few seconds, that says "You have to run Wizard before using full functionality of this application" but it doesn't say what it refers to. Any ideas ?

Hello Archer, just to say a big thank you to you, everything seems to be working ok now and all updates are installed
regards :)