Description
Qsys projects have a default setting to create a block symbol file (.bsf) during generation. When the user clicks the generate button, the tool runs a program to create the .bsf file, and then again to synthesize the project. The repeated warnings are due to the multiple invocations of the generation program.
If a bsf file is not needed, you can uncheck the option "Create block symbol file (.bsf)" which will prevent multiple launches of the tool, and the repetition of warnings.