I am pretty sure it had to do with having an older .ini file with a newer version of mame, combined with having multiple .ini files set up in my mame directory (one in the mame folder and one in the /ini folder). I was recreating the ini file, but only the one in the mame root directory, and it seemed to be looking at one I had in the /ini folder in the mame directory.
I would recommend starting fresh by moving your existing mame directory to a different location, unpacking the entire package from the mame dev site, copy your custom mame build to it if you have one, run the mame64 -cc, copy the mame.ini to mame64.ini (so Mala sees it even though it doesn't use that file, another glitch with Mala), and then make your mame.ini settings changes manually to get HLSL working (if you use it). Then make sure Mala is pointing at the mame folder and the new mame64.exe and it *should* work when you go into the mame configuration in Mala after that. At least it did for me.
Once you have that part working, start moving any supporting folders from your old mame directory into the new one. Don't move the .ini folder over unless you have a lot of custom .ini folders for individual games, and if so, don't move the mame.ini from that folder over.
I personally like to keep my media folders in a separate directory (ie snaps, videos, marquees, control panels, roms, etc), but because of Mala, I keep the samples in the mame folder.
Again, keep in mind that many of the settings, especially having to do with the d3d stuff, don't work right in Mala because much of that has changed sometime in the past few versions (possibly .154, but not entirely sure). For anything HLSL you are better off enabling it, then going into mame and using the slider controls to tweak it until you like it, then record the settings and manually transfer them into the mame.ini. Of course, once you start to manually edit the mame.ini file, you probably won't use Mala to do it any more.
For the record, I have compiled .155 and updated all my roms, but I have not yet tried to run .155 with Mala. However, I did successfully set up .154 with Mala on my last build, and taking care to be sure there was only one .ini file and making sure the entire directory was new, then moving my supporting folders into place made it go flawlessly.