I record in 24/48 and then resample and Bit dither down to 16/44, but i use CD Wave Editor to Track out each, using the same exact Cue Sheet to put the trackmarks in. I just compared a 24/48 and 16/44 of the same show(Untracked, so its the whole file)in CD Wave, and the are exactly the same in Length(time) up to the hundreth of a second.
I also use SF for my Resampling and Bit Dithering.
You want to have the Resample set to 4 (high), and also check the box to Apply the Anti-Alias filter during resample.
DO NOT check the other box for Set the Sample Rate Only.
Hope this helps.
~Rhys