Have a feeling this is going to be one of my books here.
A flash issue - or should I say one of them. Man... can't really tell you if that is an issue with flash, the site(s), the ad server dishing out the flash ads or some combination.
I doubt very seriously that defragging will take care of that issue. It could be that fragmentation is affecting the initial loading of flash into memory, but that's really above my tech level. You could probably look on the 'Files' tab in iDefrag to see if it's listed there.
While you're looking at idefrag, I can point out a couple of things about what you're seeing and my own experience. I went 3 years on my machine without defragging and not much problem. And I did have the demo copy of iDefrag on my machine during that time and checked it out on occasion.
Earlier this year my system started slowing down too much for my taste. I'd allowed it to get down to just under 30% free space. Even after moving enough off the drive to get it back to 40%, it still just wasn't back up to snuff speed wise.
You should open up the Help file with iDefrag. Head for Help - Browse iDefrag Help - Main Display - have a read over that section.
The bottom bar on the Layout tab, all that red you're seeing represents fragmented files. And, as you can see both your files and your free space (the white areas) are spread from one end of the drive to the other. That's about what mine looked like when I broke down and bought iDefrag to see if it would take care of my slow downs. Mine currently looks like this - it's been about 3 weeks since the most recent defrag:
I will say that unlike all my Windows machines over the years, on my Mac I have not "noticed" slow downs due to fragmentation until I hit around the 30-40% free space. Under all versions of Windows up through XP, I could tell the difference before and after a defrag if I hadn't done it in awhile on drives with 80-90% free space. So OS X is far ahead of the game there.
For me, it's time to start thinking about a new drive. I've found that for my own expectations, I'm not satisfied with the operation of my machine at 30% free space even after defragging. When I get back to 40% and a defrag, then I'm satisfied with it's speed. Just have more stuff that I want on the system partition and can't keep it down to that level any more.
Like I say, ymmv. I don't think there are that many as picky as I am about slow down issues and I don't believe that iDefrag is at all necessary for most users of OS X. If you're not experiencing slow downs and the beachball, it probably would produce no noticeable effect on your machine either.
edit: One more thing - always make sure you have a current backup before moving this much data around on a drive.