I've noticed this in a few videos... if you attempt to seek to a particular 'time' you're actually only moving to a percent of the video- that means the seek to time function only works if the video is exactly 100 minutes long. Let me explain:
Let's say the file is 120 minutes long. If you 'seek to' 00:20:00 you don't goto 20 minutes into the show, rather 24 minutes into the show (120*.2 = 24). Another way to test this is try to seek to more than 100 minutes- you cannot- only 99. Obviously, if the video is 100 minutes long (exactly) you are fine since you're not having to adjust by a multiplier.
I really only view mkvs, so I can't say if it happens on avis or others, but I can reproduce the problem easily.
Yes, you can get 'around' the problem by using the bookmarks function under Transcode... I just wanted to bring the problem to attention.