A couple things: First, unless you have a sample-and-hold board in front of your analog inputs there will be phase delay between the channels. The channels are being sampled very rapidly, but not simultaneously. Second, if the amplitude of one channel appears to be effecting the measured amplitude of a channel on either side of it (in the scan order)there is probibly a settling time problem. NI's cards internally only have a single A/D converter which is connected to each of the input channels through a multiplexer. Simple enough, but things start getting complicated when are doing on-board gain adjustments too. Now you have to adjust switch the multiplexer, allow it to settle and change the gain of the input amplifier. In addition, the amplifier itself has what is called a slew time, or how fast its output can change in response to a step change in the input. Put all together, if there is not adequate interchannel delay in a scan the input will still be showing the effects of a previous channel when you read the next one.
If this is the problem, there are two fixes: First don't put signals on dramatically different levels on the same card. This reduces the amount of time the DAQ card needs to adjust to each input--at the price of an additional DAQ card. Second, increase the amount of interchannel delay for the scan to give the card the time it needs to settle--of course this added time will also increase the apparent phase shift between channels so you might need to add a sample-and-hold card to get simultaneous sampling.
Personally, I would try the increased interchannel delay first to see if what you are fighting is a settling time problem as this is only a software change. If increasing the delay fixes the amplitude problem, you then can analyze the hardware solutions to determine which is the best.
Of course, if you really need absolutely simultaneous sampling, the decision is already made for you. Call NI and get an appropriate sample-and-hold card.
Hope this helps, as in a lot of things in electronics, setting up an acquisition system is a balancing act where you have to learn what compromises you can, might, should or need to make technically and financially.
Mike...