There was a big change in for r06. New a/f and timing. Here's their list of changes for each revision.
Release 9r07 (Fix for Quick adjust change made in r06) 08-20-08 9r07
Release 9r06 (support for new 06 5.7L and 08 srt8 jeep calids, ALL tunes adjusted for better launch and better fuel economy, SRT8 LX cars better wot shifts, shift points removed for 08's) 08-20-08 9r06
Release 9r05 (Fix for screen going blank after an update) 07-23-08 9r05
Release 9r04 (Fix for QA menu getting stuck on cycle key message if adjusted right after a backup has been taken) 04-01-08 9r04
Release 9r03 (Added support for new 2006 & 2008 5.7L calids, added more gear ratio choices, added more shift points for 5.7L's, added more autostick disable options) 03-31-08 9r03
Release 9r02 (internal update, NO TUNING CHANGES) 03-11-08 9r02
Release 9r01 (Fix calibration update for early 05's, Fix for import of custom tune before backup is taken, Rear 02 config parameter edited to delete all codes for rear 02's) 03-05-08 9r01
Release 20 (Fix for import of unsupported calid custom tune before taking a backup) 01-30-08 r20
Release 19 (Support for MY2008 vehicles, updated calids for 07 vehicles, Jeep AWD fix,tunes revised,axle ratio QA added, NOTE: 07 5.7L's will require you to do a calibration update after updating to this revision) 01-28-08 r19
Release 18 (Idle surge fix, Autostick fix for 06-07 5.7L,Autstick feature removed from 07 SRT8, Live data export fix, support for 06 jeep srt8(export),MBT spark adjustment added, knock sensor parameter removed) 11-19-07 r18