Well, it seems we have some problems with the interface updater task in version 1.6.9 on Windows.
The interface updater is a low-priority background task that is running permanently in the PixInsight Core application (except during process execution, where it is stopped temporarily) and its purpose is to ensure coherence of the whole graphical interface. The interface updater 'sleeps' during 250 milliseconds and then wakes up to inspect all the relevant objects and components in the whole platform. When it encounters a change from the last fetched state, it updates the corresponding GUI element (say a tool button image, a menu item, a checkbox state or a listbox item, for example). This implementation is very nice and efficient, especially in a complex application like PixInsight. This is what is not working correctly on your Windows installations, for some reason that eludes me, and the cause of the odd problems that you're experiencing.
I'm unable to reproduce this problem on Windows Vista, 7 and XP. The relation with the splash screen is indeed really odd. I'll dig into this to fix it as soon as possible; sorry for the inconvenience.