Qsys new component - file path keeps changing

I'm also having path problems with Qsys.

I have a QSYS SOPC system initially generated under Quartus 11.X (sp?).

There were problems with the hard PCIe core burst logic under Q11.X so when Quartus 12.0 came out I transferred to that and

everything appeared to work well.

Now I have another logic module to add to my QSYS system but it looks like Q12.0 qsys can't read Q11.X qsys files properly, it's totally

****ed up source file path names (I keep my source in a separate directory), it doesn't even select the top level file properly (even though

this is specified in the *.qsys file).

I'm going to have to start from scratch with a fairly complex system. :-(

Have you changed Quartus versions at all?

Nial