Hardware latency settings passing to jackd

Hello,

I've spent some time trying to calibrate latency settings in my recording system, and I finally found out that the problem is somewhere in the qjackctl area. I wrote up my adventure and it's available on the web, but Drupal won't let me paste in the link. The short version is:

Ubuntu 13.10 (fresh install)
qjackctl 0.3.10
Ardour 2.8.14

Symptoms: recorded audio not aligned with the preexisting audio / grid in Ardour. This normally happens when you don't account for hardware latency. But I did! I've used jack_iodelay to measure the hardware latency, and I plugged in the numbers into qjackctl. I experimented more, plugged in different numbers, but symptoms didn't change. I guessed that the numbers I'm plugging in are doing nothing, so I switched from qjackctl to running jackd directly. The workaround was successful: new recordings in Ardour were aligned with the grid, so the numbers I plugged in were correct, they just didn't make it from the GUI window to jackd.

Has anyone else observed this problem?

Maciej