1. Have you tried the latest stable release?
For Windows, try
ftp://ftp.kvirc.ru/pub/win32/KVIrc-3.4.0-setup.exeIt is KVIrc 3.4.0 'Virgo' 20080323 - build Apr 2 2008 18:02:50
2. To have KVIrc saving logs in the way you described, one should write an addon that would work like: globally disable logging, manually start logging to custom destination upon new query created\channel joined etc. Then (if one still would like to view those logs) the addon must represent custom log viewer, since the built-in one is hard-coded and wouldn't understand custom destinations.