We SHOULD be able to see the process it uses to deal with this transparently. The fact that nobody knows what FCP4 is doing about it is a case in point, now the SAM has left the building.
You know, Media 100 used to have the most valuable tool. It gobbled up the first couple of seconds during the digitize and examined them for audio sample rates. If it found one that didn't match the current settings, it aborted and changed them for you. Given this was with a hardware board, but this was also 1996 or 97! If the capture process could run an optional test on batch capture, and report on the sample rate. either to you or itself, it might solve a HUGE amount of trouble in this process. Instead of waiting till AFTER the capture to deal with screwy sample rates