If you find a new issue please add it to the list below by editing this page so that others can benefit from it as well. So that the formatting will be consistent, please use the Issue:Workaround format and provide short descriptive titles using the "Heading 3" format under the appropriate New Issues section.
Qsys Editor (UI) Issues
Issue: Qsys doen't remember the user-entered IP search path (Tools -> Options ). Adding the user_components.ipx as described on page 5-13 (Quartus II Handbook Version 12.0) doesn't work either. This usually occurs when launching Qsys outside a Quartus II project. The path used (in 13.0 sp1) appears to be based on the path to the QSYS file that is currently open, and not on the user's path configuration. I also observe that paths in project specific xxx.ipx files are used when qsys-edit is first run, but they are later forgotten when QSYS opens a source file (13.0 sp1).
Workaround: add a <Path path=... /> entry into the main <$QUARTUS_INSTALLDIR>/sopc_builder/bin/root_components.ipx file. Fixed in Quartus II 12.1 (The problem is observed to remain in 13.0 sp1)
Issue: Qsys Component Editor can't handle SystemVerilog packages in the top level file. Use of packages ("import mypackage::*;") causes the Component Editor to fail to find any modules.