Hi Neil,
Thanks for the comments. Al has had the same thoughts in regards to multiple core utilisation. At present, his batch idea seems to do the job of splitting the tasks quite well. Unfortunately, simply due to the nature in which autoloop works, it would be impossible to speed-up the individual processes using threads. It is a sequential algorithm (something happens and generates some data, then something else happens that uses that data, then something else happens that uses that data... so on) and it can't happen concurrently. Which means that the best thing I could do is make an application which essentially does the same thing as Al's batch file.
In regards to the cue positioning... when autoloop is run on a wave file, it removes all of the existing loops - but does not remove existing cue points. I'm not sure what you are using your samples for, but if you are using them for Hauptwerk, I always run my samples through the Hauptwerk Sample Preparation Tool (you can contact Brett Milan for a copy) before looping them. There is an option in this tool to automatically place a release marker. If this option is checked, when you "autoloop" the result, the cue point will remain in each file. I can understand your frustration in having to manually "insert" a cue point in Cool Edit for each sample.
That being said, what you have requested is a really simple feature for me to add (only a couple of extra lines of code) which I am happy to do before the next release.
Nick