you can not detect 1 MHz. search for Nyquist. theoritcally, you can not detect anything above 625KHz, realistically, it would be below that. Did you check the test panel in NI Max? There is a +5 available on pin 8, connect that to pin 68. In max, test AI ch. 0 and see if that works (should be a flat line at +5V). All your hardware testing can be done through max.
If you go to the specification for the PCI-6250 you will find that the maximum sampling rate is 1.25 M samples per second. Nyquist theorem says that you need to sample twice as fast to be able get the frequency component of a waveform. As a rule of thumb, we typically suggest to sample 10 times faster than your signal rate to be able to represent the signal with decent accuracy. A very good resource is: Bandwidth, Sample Rate, and Nyquist Theorem. What I will suggest is try to read a sine wave of the same amplitude but at 100 KHz and change the frequency from 90 KHz to 110 KHz and check if you can see the changes.