I tried cleaning out a bunch of modules I had been testing but am not using (including other wrapping modules). I have left: System, Headlines, NewBB, PiCal, iMenu, Marquee, Formulize, Formulaire, Content, AMS.
PHPDebug gives a bunch of "variable references" messages:
Notice [PHP]: Only variable references should be returned by reference in file include/functions.php line 490
Notice [PHP]: Only variables should be assigned by reference in file class/database/mysqldatabase.php line 236
Notice [PHP]: Only variable references should be returned by reference in file include/functions.php line 490
otice [PHP]: Only variables should be assigned by reference in file include/cp_functions.php line 57
Notice [PHP]: Only variable references should be returned by reference in file class/module.textsanitizer.php line 257
Notice [PHP]: Only variable references should be returned by reference in file kernel/module.php line 123

I'll try a fresh install on a less cluttered site and see what happens.