We (well ok, a customer) found a problem with delay compensation.  Sometimes, it doesn't actually compute the correct delays.  We have a fix, see below.  Let us know if it does or doesn't work for you.  This fix should be safe, we plan on including it in the next release but I wanted to get it out now in case someone else has been wrestling with this.
Download this file:
peaveyoxford.com/pion_compiler.exe
Put it in the following location:
C:\Program Files\MediaMatrix\NWare 1.4.2\plugins\pion
You may want to backup the old pion_compiler.exe first just in case.
Note this this is only required if the project has "Auto-compensate signal delays" selected.