If you have a patch that takes "250% of the CPU" or something like that, and it doesn't use the microphone/linein, and only writes to a file, then Pd should be able to do that flawlessly, if no objects use physical time, that is, they all use logical time instead. Logical time slows down when you use "more than 100% of the CPU" to account for the fact that only 100% of the CPU is usable (!) and it catches up on physical time when you allow it to.
Interesting. This explains to some weird behaviour I noticed with patches that I use mainly to trigger MIDI synthesizers. If I have set the audio buffer too low, then it my clocks run way too slow. I always thought that pd goes crazy when it can't deliver the requested latency but your explanation makes very much sense to me.
Best Urs