First, it depends what you install. If it uses the Mac installer, then, maybe, yes (or anything from Adobe.) But certainly not any software. There are times for running Permissions repair, but Permissions repair is NOT needed for general maintenance. You won't be doing any harm, but you will be mostly wasting time.
Read this.
http://unsanity.org/archives/000410.php
Now, as for repairing from the DVD. This is completely wrong. Since you have installed the OS from the DVD, you have doubtless updated to a different version, there have been security updates, Java updates, you name it. All of these will have changed the actual Permissions database on the volume you are running from.
If you repair from the DVD, you are ignoring all the changes that have been made and recorded, and you are actually introducing errors, rather than correcting them.