So I believe that advance and abandon are now working off "base character" levels, i.e. levels not including any level-adjustment, while experience to advance is based on base character levels + LA.
I've already updated the stats command, so it should also be based on base character levels, and I need to go through and update the other following features. Included are my thoughts on the changes I should make, though my thoughts will be obvious, almost everything should be based off base character levels except experience needed to advance..
Skills: need to work off base character levels ; Some LA races might get additional skill points, mewbe, but these can be handled on a race by case basis.
Wear / Wield are currently going off +LA character levels, these will be also adjusted to work off base character levels eventually. I'm dragging my feet on this so we don't get people who suddenly can't wield signature weapons or whatnot.
Hit Points - I've seen code for two methods of resolution in the code, I need to dig in and check which is currently working, and whether or not we should be granting HP for LA Hit Dice (I could go either method, though again, also willing to handle on a race by case basis.)
Please let me know if you think I'm off-base on any of my assumptions, but I think going on the base character classes for everything but advancement is what I intended when I put in multiclassing.