I am just wondering if all these issues are not linked to a same error that would be: we loaded an old version of the software on the spacecraft.

It can be quite common in the space industry to load non-flight or old versions late in the AIT phase in order to test on other modules, or even just to officially close old actions. But before delivering everything we would check all the versions, and make sure that everything is as expected and most importantly, as described. If that step was screwed up, it is bad news for the QA, but that would explain why the errors could be found and fixed quickly: it meant just going through all the non-conformances and change logs and understand what was different between the version used, and the version that should have been used.