I didn't try the patch, but I looked at the source code (current svn, revision 11896) briefly, and noticed that envrms~.c doesn't use CLASS_MAINSIGNALIN(), so maybe the dsp stuff isn't initialized correctly.
That's interesting, and I think it is a clue to what is going on, but it is [envrms~] that makes the signal come _out_ of [clip~]. Without this connected it doesn't go from [clip~] to [svf~] even though it is directly connected. That's why this is a confusing bug. It is as though the [envrms~] acts like a siphon, opening the flow for the signal to travel, but doing it remotely as the [envrms~] just goes to an atom, and does not play a part in the signal path or control mechanism of the synthesizer. Interestingly enough, this does not happen with the nogui version - [clinok~] - only the gui version - [clinoker~] I'll have a look at svf~ to see if the bug is there.
Cheese, Ed