Live recording sync/phase/tuning dilemma

[ftdrummer]

https://www.dropbox.com/sh/h99kzm46j79jqj7/I5lUGB1RYg

Here's a snippet of a gig I recorded with an RME UFX and a FF400 unit over ADAT. As you can hear, the bass and guitar seem to be out of tune, but particularly on lower notes. Now, I was mixing the live set too, and I'm sure we would have noticed if they were that out of tune on the night. Has anyone here got another explanation through some sort of phase or sample rate anomaly? The files were recorded at 48k/24 bit to both Cubase and direct to HD, and sound the same. The only other thing I can think of is that I'm running the Cubase session at 48/32 bit.

Another strange and annoying thing that occurred with the recording was that the channels that were recorded on the FF400 over Adat were littered with what seemed to be timecode/sync pops, and I have manually edited them out. I don't know how this happened they were wordclocked and appeared to be stable.

Any help would be much appreciated.