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Noise issues with NI PCI - 6281 Analog input



I am using NI PCI-6281, for precise voltage acquisition. 
When I connected the 6281 Analog-Input to an external voltage reference the acquired signal noise span is 3 mV. As I was surprised, to cross verify, I connected this voltage reference to an Agilent 6.5 digit DMM. The noise span observed on the DMM was < 10 μV. 
Then again, I looped-back a voltage output of 50 mV from the 6281 Analog-Output to the Analog-Input, this time I observed a noise span of  100 μV (at +/- 100 mV range, 1 kHz DAQ rate, low pass filter enabled). 
Why am I experiencing such large spans of noise when connecting to an external voltage reference and comparatively very little with a loopback? Any help will be appreciated. Thanks.
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