I'm moving all my DVD's onto NAS for media center playback, so I'm wanting good quality, and I'm wanting rather consistent quality.  Maybe I'm going about things all wrong, but I've been using the target file size to determine the bitrate for acheiving a 100:1 bit/pixel compression ratio with the maximum video size and then using a standard set of codec settings for x264 that I found as recommended to get high quality encodes.  I'm also running an Intel Core2 6600, so using codec settings to specify 2 threads is a must since FU on it's own doesn't seem to care and only uses one core.
The oddity and my question is that I've noticed if I ignore the video encoding size at something like 1500KB, but specify a target rate of 1300Kbps in the codec settings with codec settings selected rather than encoding speed, a 30 minute TV episode comes out at around 1500KB.  I've also noticed that if I que up a bunch of movies and configure them by adjusting the target size to find the bitrate with 100:1 compression, the target bitrate in codec settings doesn't save with the FU project.  So if I que movie 1 with a target bitrate of 1700Kbps, que movie 2 with a target bitrate of 1300Kbps, then go back and edit movie 1's project settings the codec settings come up with 1300Kbps or whatever I last set.
FU seems to be paying attention to both since I get two core utilization with codec settings but have the file size oddity if I don't adjust the target file size.  My major issue is that not all my movies are the same aspect ratio or resolution and I seem to be getting hit-or-miss quality with some movies looking flawless and others exhibiting blocking issues on playback.
Am I completely misunderstanding how to go about encoding with FU?  For my application a specific file size is not as important as consistent close to original video quality.

Thanks,

G