決定ボタンの件について少し調べてみたら下記commitが原因だと分かった

Blind workaround for Shining Ark circle button problem
https://github.com/hrydgard/ppsspp/commit/21647cd3c1505258a016dfa9f420ee4a1f8b5dee

とりあえず以前の仕様に戻したいなら「Core/Dialog/PSPDialog.cpp」のreturn部分2箇所を変更すればOK

int PSPDialog::GetConfirmButton() {
 if (PSP_CoreParameter().compat.flags().ForceCircleButtonConfirm) {
  return CTRL_CIRCLE;
 }
 //return g_Config.iButtonPreference == PSP_SYSTEMPARAM_BUTTON_CROSS ? CTRL_CIRCLE : CTRL_CROSS;
 return g_Config.iButtonPreference == PSP_SYSTEMPARAM_BUTTON_CROSS ? CTRL_CROSS : CTRL_CIRCLE;
}

int PSPDialog::GetCancelButton() {
 if (PSP_CoreParameter().compat.flags().ForceCircleButtonConfirm) {
 return CTRL_CROSS;
 }
 //return g_Config.iButtonPreference == PSP_SYSTEMPARAM_BUTTON_CROSS ? CTRL_CROSS : CTRL_CIRCLE;
 return g_Config.iButtonPreference == PSP_SYSTEMPARAM_BUTTON_CROSS ? CTRL_CIRCLE : CTRL_CROSS;
}