As you may have seen in pyxform and at Form conversion from XLSForm will no longer generate ODK XForms inline selects, we recently merged a change to always create secondary instances for selects to support exactly this usage. It also makes pyxform code simpler and makes form definitions smaller.
Unfortunately, it has led us to identify a number of issues in Enketo ranging in severity from cosmetic (the issue you linked below) to likely serious. We're still working on how to approach these unexpected findings.
This looks like a new issue.