In two different cases, administrators reported that fisheye was not scanning certain areas of the repositories, but there were no errors and the repository settings were correct.

Later we checked the repository defaults to find that some other person had accidentally defined an includes or excludes and not cleaned it up.

Any repository default settings should be displayed when viewing the repository to reduce confusion.

Fisheye knowledge base entry opened for this issue:

http://confluence.atlassian.com/display/FISHKB/Fisheye+does+not+scan+all+of+the+repository