I had a similar problem a while back. The culprit for me were a bunch of 0kb ghost cache files that had been created at some point. Once I deleted all the 0kb cache files, everything worked again.
Unfortunately I don't seem to have the same issue. I cleared out my entire cache file and rebuilt it, and it still froze. In fact it freezes more often, when loading banners now. After letting it sit for ages and freezing every 3 minutes, it no longer freezes since it created the entire cache.
I'm using Hermes IOS222, so it might be a contributing factor (or not). I might end up going with d2x, but my HDD falls asleep and doesn't work properly with it, so I might need to buy a new HDD.
Does anyone have any good recommendations for a HDD that will work well with WiiFlow? Price doesn't really matter to me...