Permissions not staying repaired

Yesterday I did software updates to my desktop iMac. There was a set of updates done which came up on my Apple menu software updates which included Mac OS update to 10.7.5, iTunes 11.0.4, Epson printer 2.1.3,Remote Desktop Client 3.6.2. I ran permissions prior to install, disabled firewall and ran permissions after with restart. Prior to the restart there were MANY found permissions that were off and at the end said Permissions Complete.

I then proceeded to the next set of updates which included Security Update 2013 -003, Safari 6.0.5, Airport Utility 6.3.1.

I believe the updates all downloaded without problem.

There was, however, the screen that said, Restart your computer, and I inadvertantly hit Not Now or something like that, not paying attention as I was writing down the software updates that I was doing. I then got the window back to restart and thought that was all good. Did I cause a problem with the downloads by the first decline to restart to finish the install?

At any rate, I did the permissions following the second install group, and again saw MANY permissions the same as for the second group. I have attempted to run the permissions a number of times thinking it would eventually take care of everything - It did give the message Permissions Complete (or whatever the message at the end says to verify it has taken care of all needed). I restarted, tried again with shut down, and still the permissions needing repair come up.

Most of them appeared to be involving Monitor and other lanquages.

Why wont the permissions stay repaired? I have run it again this morning and the same things come up. I did believe the message following the first updates and so am not certain if the problems were a result of the first updates or the second. I did look at the console and tried to compare the permissions needing correction (and completed) with all of the disk utility runs. The one that stood out as different was something that said Apache 2, am not sure which run that came in. I don't even know what Apache 2 is.

Also, following Apple suggestions, I was doing the groups of software updates as it said to do in order untill the check for updates came up as "Your software is up to date". Which it did. I wonder why it had me do the Security Update 2013-003 and not the 001 and 002? Does the third one cover the previous two?

Do I need to worry about those permissions contiuing to come up?

I hope someone can help me with instructions that are fairly simple, I do not feel I am very saavy at this point.

Thank you in advance.