i had some problem with a -nogui patch running [delwrite~],[delread~] pairs.  it was a C programmer who eventually fixed the problem for me, but if i recall correctly, the issue was with the delayline samplerate not being set properly when pd is running nogui.  running with gui seemed to introduce a slight delay which caused delayline samplerate to be initiatlized properly. 

i wouldn't be surprised if your freeverb~ problem is somehow related, as it also uses delaylines.