Are you talking about the field labels that come from the aliases (FieldName) or the content (FieldValue) of one of your fields? Which HTML popup XSL are you using? If it is custom code, there could be an error in it. Do a View Source on the popups with problems to see if the XML has the contents you would expect for that record.
Can you tell me how I would vew the source code of the html popup? I can view it in the KML file and do not find anything wrong (other than the field aliases being truncated).
Rob
This is sounding like a little ESRI bug when generating or transforming the XML; XSL does have a replace function that could take out one letter, I suspect because you have spaces in your aliases.
To look at the popup source: View Source will only show you the XML. I use Firefox with Firebug (this is a miniapp that can be added to Firefox) to view the hidden HTML. This requires navigating away to a new tab from the XML page and then back after opening it in Firefox. Right now, this isn't working for me because Firefox is not playing nice today, but it was when I was developing my XSL.