I think this sounds fairly close to what I was doing.
I ran the test again using both a USB-6008 and in house logger in parrallel, still getting the weird readings with the USB-6008, but the in house logger is working fine.
The only difference is that in front of the in house logger I am running a 2 to 1 voltage divider because our loggers can not handle more than a 3V input.
The 5V wave actually runs at 1/8 Hz because it is an address line to a multiplexer, and the address changes every 4 seconds. The logger may read different voltages on the first and last of the 4 points it should aquire during each half of the cycle. The weird points I'm getting are in the middle of the cycle. For example on the rising edge it may read 2.5, 5, 5, 1.9 in a typical sequence, the weird ones are more like 5, 5, 1.4, 5. Or 0, 1.8, 0 0.
I am not sure if I can more fully explain what was happening.