Thanks Christof and Roman for the clarification, now I understand it a little!
Actually, before Pd 0.52, the polling scheduler did not really work
correctly together with the Jack backend, i.e. the "Delay" setting was
basically ignored and it just did double buffering. This has been fixed.
Anyway, Pd should make sure that "Delay" is not smaller than the Jack
buffer size, thus preventing silent output. If that's not the case,
please file a bug report!
You're right! I was using a 10ms delay with 512 buffer size / 3 periods on Jack.
As soon as I changed to 12ms DSP worked normally. I used 10ms on Pd for a long time, but it was ignored as you said, and now it has turned into my "problem".
So, that is not a bug, but maybe this limit should be clearly stated somewhere to avoid confusion.
Thank you all so much!