Hi, wreckage
I guess you do not have any anti-aliasing signal conditioning before SCB-68.
The 4 or 5kHz noise you saw may actually be the noise at a much higher frequency. I have some experiences from engine cell projects that an MIO card would measure high noise level, a DSA card (eg, NI 4472, which has anti-aliasing filter) returned very clean signal.
Unless you are sure that there is no high frequency noise above half of your sampling frequency (Nyquist frequency), you probably need to use some kind of anti-aliasing signal conditioning.
Also, have you tried differential instead of RSE?
Regards
Ian Ren
Roush Industries