Shrinking Graph Area
Sometimes zooming in or auto-ing out (zoom to fit) cause the graph area to shrink. The graph should settle down to a stable size after a few goes of in and out zooming.
Axis tick marks
Sometimes, on first running the axis tick marks and/or waveform labels might be a bit messed up (i.e. not line up correctly), especially on first zoom. Zoom out ('a') and in again (mouse drag). Resize the graph area a bit via its bottom left corner if tick marks go off the graph area and onto a clean bit of the schematic page if necessary. Double click on graph and OK again may also be required. Once fixed up it should remain ok.
Incorrect Data readout
This occurs when 2 graphs display the same data set. If a graph on the schematic page and the same graph type (ac, tran, noise) on a graph page, then the cursor readout values may be incorrect on one of them, although the axis on both may be correct. This is because both graphs use the same database. Press the "a" button to force an auto scale of on the current graph being looked at.
Misc.
Manual graph ranges settings get quantised to sensible values, the actual values are not directly used. This can be disabled, by double-clicking on the graph, selecting the options/misc tab, and clearing the "Enable axis scale quantisation"
Make sure that FFT/IFFT data has been calculated for the signals of interest by pressing the appropriate buttons. (see the help section on the Fourier stuff)