I'm not 100% what both the issue and the fix seemed to be. I did try to change the alignment time mid-alignment but as you mentioned it didn't react to that. I think a combination of flipping IRS switches multiple times, not pressing the align button on the fms in a timely manner, and changing the align time on the efb. One or more of these ended up fixing it after some time. I'm sure it was user error. I'll try a fresh flight again soon and see if I can get it to work normally.