I'm sat next to Toby and he asked me to try and answer this for you as I've been using them far more recently than he has.
Firstly, when you say it sounds during pre-measurement, are you referring to the high pitched tone, or the sound of the fan flushing the chamber? I've never experienced not hearing the high pitched tone before, but I think so long as you can hear the fan flushing the chamber, that is the most important part of pre-measurement calibration and it should be OK and if the results look reasonable, then this is encouraging.
Secondly, it sounds as though you are implementing partitioning experiment protocol 1 (with 4 sets of 9 tubes)? I'm not absolutely clear what your question is, but essentially, if you have removed litter before taking an initial emission measurement, you can replace the litter that was removed (same amount) from the tube, wait for some time and take another measurement, which will include the flux from the litter. Then you can remove the litter again, wait some time, and take another measurement. The difference between these two measurements is attributable to the litter.
I hope this helps, but please tell me if it wasn't what you were asking for and I'll get back to you again.
All best from Oxford,