See here for an example I posted earlier today.
http://exchange.ni.com/servlet/ProcessRequest?RHIVEID=101&RPAGEID=137&HOID=5065000000050000007EDD0100&HTHREAD=000122238&UCATEGORY_0=_49_%24_6_&UCATEGORY_S=0
I will venture a guess that the t0 values of the waveforms are not monotonicly increasing values.
If the t0 found in a new waveform that is presented to a chart that already has data plotted that contains the t0 value, the chart will be cleared an a new set of plots started.
The other thing that will make waveform charts start over is if the number of plots changes.
Just guessing,
Ben