I have the April 9 version of builder64 installed. I've found that DB64 still seems to have problems remembering texture changes sometimes, and will revert them to what they used to be somewhat randomly. There are a few things I can note about when I've seen this behavior.
I've been copying and pasting textures in visual mode. I've been going in and out of visual mode frequently. Also, I've been saving the wad under new filenames frequently (I always do this often so I always have several backups to go back to if necessary).
I think that it has to be related to either going in and out of visual mode too much, or perhaps saving resets textures somehow (in fact I'm strongly wondering if saving is what's doing it). Pasting textures, going in and out of visual mode, and saving where about the only things I was doing when I noticed some textures resetting.
I installed the April 9 version of DB64 over an older one (the one from before the slimdx trouble showed up). That couldn't have affected anything, could it? I don't recall hearing anywhere that you have to uninstall the old version before installing a new one.
Edit: I did a little more on the map, adding some vertexes to some linedefs, aligning some offsets, and changing textures in visual mode. That's all I did other than saving. Nothing with the textures went wrong until after I saved.
After saving under a new filename, going back into visual mode I now saw some textures had reset. I really do think it's saving that's causing this.
If I reopen the newly saved map the textures are correct again, so it's saving correctly. It's just like something gets reset in memory after DB64 finishes saving.