Hey Steve,
The MIO-16E-1 has a maximum sampling rate of 1.25 MS/s, so if you're using that device you'll be able to sample that fast.
Source impedance is usually an issue when acquiring from multiple channels, but it could be causing problems here. If your source has a somewhat large impedance (around 1 Kohm or greater) and you are sampling at high rates, then you might be running into charge injection of the instrumentation amplifier. I would take a look at the document linked below that describe using a non-inverting buffer to decrease the source impedance dramatically.
Using a Unity Gain Buffer (Voltage Follower) with a DAQ Device
http://zone.ni.com/devzone/conceptd.nsf/webmain/CD57A73721E0612586256BAE0055CDD9?opendocument
Regards,
Todd D.
NI Appl
ications Engineer