Ok, I'm reverting back to QII v9.0 and SOPC Builder and Nios2-studio because they all worked. The SDI Audio extract and embed are not worth it, Qsys is extremely slow to generate, and randomly works or doesn't, and Nios2 Eclipse build tools can't remember your Flash programming settings from one minute to the next (though apparently, if you create an empty flash settings file, and save to that, then it will work, but not the handy list of projects you got with nios2-studio).
Also the VHDL editor in QII 11.0sp1 is a retro-grade step from QII 9.0. The gripes I've got so far may not sound much but make some things much more laborious:
1) Column block editing is broken. You can select, and cut and delete column blocks, but pasting fails completely - it doesn't think you want your pasted block inserted as a column on the lines that are already there, and instead pastes them into new lines. Ha ha ha
2) You can't get a split screen in the editor anymore, so comparing your component declaration to the instantiation is a pain in the a**e.
Qsys:
1) The tristate bus problems seem to be well documented here:
http://www.alteraforum.com/forum/showthread.php?p=119780#post119780 (
http://www.alteraforum.com/forum/showthread.php?p=119780#post119780)
but since then I've compiled my design, which after that thread had programmed flash beautifully, and not having changed ANYTHING in Qsys, only to find that the flash programmer can erase my flash, and program the first 120 bytes or so, but then gives up. This is on a board that I've compiled and recompiled multiple (at least 20 different) designs for in QII v9.0 and SOPC Builder and NEVER EVER had that happen.
2) Qsys seems to take an AGE to generate. I assume it's all the inserting Merlin stuff between all the avalon components, etc. But I suspect they introduce timing problems with my flash programming as well, so are not worth it.
3) All the memories I had generated for v9.0 don't seem to work, and there doesn't seem to be any way of adding a "this is a memory" tag to a custom component. Fortunately the memory generator in Qsys seems to let you generate internal memory relatively quickly, though you get many more signals than you used to in v9.0
All in all, not a happy chap.:(