Well this might be caused by a naming conflict where a class may have the same name as a package. Let's visualisze that. If your folder/file layout contains anything similar to the example blow, try to set the SafeUmlExport
flag in the Configurations.
+Toolbox
...
|- +Tools
|- Hammer.m
|- ScrewDriver.m
|- Tools.m
Notice how there is a conflict between the class Toolbox.Tools
(File: +Toolbox/Tools.m) and the package Toolbox.Tools
(Folder: +Toolbox/+Tools).
This is related to a limitation of the plantUML.jar. Please check the FAQ of plantUML:
I want to generate huge diagrams! - plantuml.com
See the command line options of plantUML.jar: http://plantuml.com/de/command-line