Oh I just had a thought! Depending on your pitch/time stretch options, it could be so, than upon importing audio that is say 110bpm, if the file contains tempo information, a fresh project of 120bpm may automatically time stretch the imported audio clip causing a rise in pitch if you have the settings set a certain way both for how Cubase deals with importing audio and with how it applies time stretch.
If you have it set to musical mode and some other options (I forget exactly sorry) like “make imported audio match project bpm” (that’s far from it’s real name, but that’s what it essentially does). Mixed with a tape style time stretch setting could cause the issue you are explaining IF fruity loop’s default tempo differs from Cubase slightly and it automatically adds tempo definition to exported wav files.
It would then pitch up the imported audio by a bit to match the BPM you have as default, by shortening and speeding up the track slightly with time stretch.
Here is someone else who had the same issue from another thread (they also point out an issue specifically with importing FL files they had too)…
"It seems to depend where the file comes from. I had a bundle of files from Fruity Loops to incorporate into a project and they were all warped. Fairly easy to see the little logo on the region and also check in the Pool.
"Should be an option somewhere like “Auto warp audio files on import”
OR
“By any chance is your root key selected? That might be causing your problem?”
Look the most promising! …
There’s also some stuff about ACID files with tempo and key data that appear as .wav files and if left on default by the user printing them can throw off your project when opening them as cubase thinks it needs to change the key or the tempo of the track. That may be it too … lots of interesting stuff on that thread that could all well be something to do with what you are experiencing. I’d read the full thing…
Hopefully this is the fix for you!