Robot, let me add two things;
1) get beta r344 from this thread
2) make sure you are not transcoding the files that have this "slow seek." Make sure you are instead streaming them (assuming they can be steamed, as with most .avi, .mpg etc) You can do this by adding "avi,divx" etc to the option "skip transcode for the following options" under the Transcoding tab, and Common Transcode Settings section. FWIW, I added "divx,avi,mpg,mp4,m4v,m2ts" (no quotes) to my skip field, and "mkv,wmv" to my force transcode field.