I'm running MenuMeters, so I can see things like network throughput, CPU usage, RAM usage and disk activity. While OGP4.2.2.b2 is paused, the CPU is pegged (as I said,) and I can see the RAM usage fluctuate wildly, usually filling up completely, with a ton of write disk activity, and then RAM clearing out right before the app becomes responsive again. BTW, this behavior isn't isolated to this iBook G4. It also happens on a dual 2.3GHz Power Mac G5 with 4.5GB RAM, fresh install of Leopard from a bare disk, and no previous preferences. Just a quick note to let you know that I've found a workaround. Fortunately, I had exported Visio XML files of all my.graffle files before moving to Leopard.
Omnigraffle 2.1.2 Beta 1 For Mac

Omnigraffle 2.1.2 Beta 1 For Mac Torrent
I opened one of these up in OGP4.2.2b2, and saved it back as a native.graffle file. It's now 2.8MB, which is more like what I expect. I've been working with it, and the size seems to be holding steady, not growing out of control. FYI, I looked at the contents of the 68MB version of the file (same visual content,) and the data.plist file is almost 67MB, the rest taken up by bitmapped gfx I have embedded in the file. The 2.8MB version of the file has a data.plist inside that's only 40KB. The odd thing is that the original.graffle file I started with was still only 2.8MB, and had been generated in OGP4.2.1 under Tiger 10.4.10.