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Can you describe how it "stops indexing"? eg. does it finish and create the index files, or does it just sits there like its still looking for files (and does so for a very long time)?
If this continues to happen, save the index log after indexing ("File"->"Save index log to file"), make sure you have Verbose mode on, and e-mail the log as well as your ZCFG file to us via zoom [at] wrensoft [dot] com.
Think we've found the problem. It's actually when you have a start point which fails a CRC-32 check. Zoom then doesn't realize it should move on to the next start point (or stop indexing).
We'll fix this bug in Version 4.1. In the meantime, you can remove this start point (http://www.wdf.org/) or disable CRC-32.
The reason it fails, by the way, is because of http://www.conway.com/wdf/ which was indexed earlier and is the same page.
I also looked in the logs, it shows that it found and indexed the http://www.conway.com/wdf/ path earlier, and the new log with the skip instruction shows no evidence that the sring "http://www.conway.com/wdf/" was read.
Perhaps another URL somewhere else on your site (or one of the ones you're indexing) has another copy of the same page?
What you should try to do is, re-arrange your start points so that "http://www.wdf.org/" is first. Because the order of the start points change the order in which pages are indexed, it would allow this site to index first, and then the other "copies" of this page will be skipped accordingly.
Just to clarify - the skip pages list does not support wildcards (eg. "*"), it serves more like a list of keywords which is matched against the URL. There are some examples in the Help file if you need more info. Hope that helps.
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