Until PowerMail version 6, only the text part of messages were indexed, which precluded HTML messages with no plain text part (a practice that used to be frowned upon) from being indexed. Society evolves, so do developers. 

Note that this is a feature that can be turned off and on, since malformed HTML messages may crash Apple's method for extracting HTML (NSAttributedText for developers out there) and hence crash PowerMail during indexing. 

(This is a problem that we had also seen in FoxTrot Professional Search, which however is structured differently internally).