...All players are assigned to 1x.  If I change them they aren;t saved for the next time I enter mame.
Or do you mean you always used commandline switches?
splitmouseaxes vs 
switchmiceaxessplitmouseaxes: (Automatic setting change) If set, MameAnalog+ will 
override any saved changes, much like 
resetmouseaxes.  It's designed so to set both player one axes to mouse 1 X axis, both player two axes to mouse 1 Y axis, both player three axes to mouse 2 X axis, ect.
switchmiceaxes: (Manual setting change) If set, allows you to switch player axis to mouse axis mappings in game.  Much like 
switchablemice, but you switch by the axis (vs 
switchablemice by the mouse).
Ideally, if the mice are set up perfectly, you could set 
splitmouseaxes the first time you play the game, analog+ will save this, and then no need to set it again.  
Realistically, the best time to set 
splitmouseaxes is for 2 spinner games and either 
singlemouse set (win9x) or 
multimouse_winxp not set (winXP).  This setup, you know you will have the X & Y axes split between players 1 & 2.
Almost the same with 
switchmiceaxes:  ideally, you'd only need it set if you haven't set up the game yet.  Once you set up the mice axes for a game, you don't need to change it any more, so you could leave this not set (and also not set reset or split).  If Analog+ is working correctly, it would read the saved mouse settings (and as long as you didn't change the mice), and have the last settings.
However, you're saying all players get mouse 1, X axis when you set 
splitmouseaxes?  I'll look into this...