I too have exactly the same problem, for as long as I can remember Compressor 4 has never finished processing a job there is always 1% to go. However when you check the file it is complete and working. I can only assume it is a bug that they cannot be bothered to fix as no update has addressed this problem.
I also am experiencing this problem. I am trying to compress from Final Cut Pro to make an MPEG 2 DVD which is 2hrs and 18 minutes duration. The processing seems to never complete even leaving it overnight. I would like to find out if there is a limit to the duration that a dvd can run on Compressor. I have looked at the settings for MPEG2 for DVD and it seems to be 123 minutes maximum. Surely there must be a way of changing this to accept longer runs? I have reoorded a stage show which runs for over the two hours length.
Select the video strem in the batch window and open Inspector. In the Encoder pane click on the Quality tab. Select the desired mode (CBR or VBR). Click on the gear to the right of Average Bit Rate. Move the slider to the left and note how the "allows up to" message changes. It's not exact, so give yourself a decent cushion.
Do some quality tests. Open the Preview window and set in and out points to select a short section. Encode and adjust as necessay. Read the chapter on Frame Controls if you haven't already. Knowing your way around Frame controls is often the difference between a passable result and a great result.