It seems that whenever I load a patch that uses a "pd *" style subpatch, the subpatch window always opens as well, when the main patch is loaded.
This should happen only if the subpatch was open when you saved the main patch.
As for your question about the delay behavior.. On my system delay is accurate to +/- 2 ms.... which I would expect with a blocksize of 64 samples. Maybe you are using a large blocksize?
The clock rate of /dev/rtc is controlled with ioctls by user programs... its not fixed by the kernel... pd probably sets the rtc according to the blocksize in use... unless it uses some other method, I don't know.
ciao andy