I'd chalk it up to some sort of corruption in your existing ini files. Sigil 0.9.11/12 raised the possibility of ini file corruption to brand-new heights, but it's not impossible that your 0.9.10 inis had some corruption, too (even if they were untouched by sigil 0.9.11/12). There's a rich history of QSettings botching things over the years. And deleting the Sigil.ini has always been a go-to method for trouble-shooting Sigil issues.
Just happy it's working for you
now!