I think I found a crazy bug. Unless I'm going mad.

I only noticed this because there's a bell in this footage. When I bring it into the timeline the ringing it's a semi-tone lower. What on earth could cause this?
The footage is 48 kHz

Is the bell footage the same frame rate as the project?

Yep. 

It wasn't in the original (see video above) it was 24fps vs 25 but I just made another project at 25fps and it's the same. 

Crazy, eh? 

jamespeach wrote:

...When I bring it into the timeline the ringing it's a semi-tone lower. What on earth could cause this?

In the example you posted, you can see the project is 23.98 fps and the clip is 25.0 fps. The algorithm for rate conforming 25 to 23.98 is to slow it down about 4%.

I realize you said you created another 25.0 project, put the 25.0 clip in it and the same tonal change happened.

Please double-check everything you did. Create another library, import that clip, and carefully create another 25.0 fps project using "custom settings". Verify in the Inspector that the *custom* project remains at 25.0 fps, then add the clip. Make sure both project and clip remain at 25.0 fps. 

If the audio tonal change still happens, select the clip in the timeline, examine the audio properties in the Inspector for that clip. Hover your mouse over all the grey bars separating each element of the audio inspector. You'll see a "show" command appear. Show or unhide each element of the audio page in Inspector. Make sure no audio effect, noise reduction, etc has been automatically applied.