There are about 43,000 pages. Yes, it is being rewalked. I've set the crawl delay to 1.2, with 1 thread and 2 servers in order to lower the load on the server. It now takes about a day to walk the full site, so there is almost always a rewalk going on. Right now, it is doing a full walk. I just upgraded the software, and planned to try the refresh walk again.
If you were doing a refresh walk with the version 4 software it may have caused the higher load. The Version 5 refresh is significantly better, and should not cause as much load on the system.
It was version 5, but I was doing a new walk (I was having some trouble with refresh, It is scheduled to do a refresh walk next time, so I'll see if that helps. We were also getting some timeouts with refresh walks before upgrading to version 5, but I'll see if the new version 5 refresh eliminates the problem.