Sounds like maybe FFXIV is reading the actual button press (ex: the "5" button) and the mouse driver is sending your mapped/macroed key (ex: the "alt+5") as well. Maybe there is a setting in the mouse software to prevent this.

I have a Razer Naga Epic which also has 12 buttons. I use mine a little differently, but maybe this would work for you if you can't get it to work the way you originally wanted to. I don't map the mouse 1-12 buttons to anything in the mouse software, which by default just makes those keys translate to 1-9, 0, -, or =. In other words, it'll send the default keymapped values for your main hotbar. I have multiple rows of hotbars, and I've keybound them (in FFXIV) to Ctrl+<number> and Alt+<number>. I can then use any skill from my hotbars by pressing ctrl/alt (if necessary) and the button my mouse.