I have a couple of suggestions and questions for you. First, do your device's output signals comply with LVDS standard voltages? Assuming your outputs are terminated with 100 Ohms, what is the expected common-mode voltage between the positive and negative legs of the signal? Also, what is the expected voltage swing between the high and low voltage levels? When you set up the static generation channels, do you then also write '1' to all of those channels like in Figure 9 (http://zone.ni.com/devzone/conceptd.nsf/webmain/87c36c9f09bf61e886256e460067bb1b)?
In general, the acquisition and generation techniques described in that application note were not intended to be used at the same time on a single 6551. The reason is that all generation channels (including both dynamic and static) use the same high and low voltage settings. Setting the generation voltage for either the static or dynamic generation channels will actually set the voltage for all generation channels. In the sequence that you described, your dynamic generation channels are probably outputting voltages of 0 and 1.2 V, although this seems to still work for you. You may wish to check the inputs of your device to make sure that a swing of 1.2 V will not eventually cause damage. If you need to, you can change the low voltage from 0 volts to better fit the dynamic generation (for your device's inputs) since that level is not used for the static generation (all of the static channels are set to logical '1').
I hope that helps clear things up as opposed to making them more complicated. Send a reply if you are still running into trouble.
I wanted to briefly clarify my previous comments. The 6551 is capable of performing dynamic acquisition and generation at the same time. The generation voltage settings of 0.7, 1.2, and 1.7 V cannot all be used at the same time.
A 2nd board would certainly help (and multiple 6551s can be synchronized very easily), but it sounds like one board may still work for you if your device can accept 1.2 V and some other voltage level for its inputs. Based on your first post, it sounds like your device is capable of acquiring data with the settings of 0 and 1.2. Also, keep in mind that the output impedance of the 6551 is 50 Ohms on each channel, which will cause a noticeable voltage drop if your device is terminated with 100 Ohms.
I have one more comment about your first post. When you close a generation session, the 6551 will continue to drive the idle state on its lines. By default, the idle state is "hold last value", so the last value of your waveform will persist past a Close. Once you close the session, you can reopen it to take back control of the lines, or you can reset the device to put the lines into high impedance.