I have been struggling with this for a few days now. My blog aggregator http://stata-bloggers.com/ for some reason posts some excerpts as the full texts while other excerpts as the 100 word specified auto-excerpt. I am using also the plugin (Thumbnail For Excerpts) to ensure that when possible the posts display a thumbnail.
I don't think this plugin is affecting things since after disabling it there still seems to be the same problem. I have tried using other themes as well and they seem to suffer from the same issue. Most recently I manually reinstalled wordpress, replacing the admin and includes directories.
Any suggestions would be greatly appreciated.