One machine logs cs-uri-queries using + as the space and another in the same farm logs them using %20
I only noticed when searching for a specific document being accessed - one server was giving out 0 hits, which I thought odd, given that the farm is supposed to be load balanced.
I'm guessing its an IIS configuration rather than a logging issue - any ideas where this is set?
Grab the Web Deployment Tool and compare the servers.
You can use -verb:sync and -whatif to compare the configurations.
If you have a health check on your load balancer the one without any traffic may be failing the health check. That would explain the traffic differences.
As for the root cause differences, does one have URLScan while the other doesn't? Or it could be other config changes that set them apart. TristanK's suggestion of WebDeploy is a good one to do a diff.