Sometimes issues like this can happen at anytime so it's hard to tell exactly but what we can do is try and pinpoint as to why these things happen and the usual case is either mod-related, a bad installation and/or messing with files which leads to issues down the road (so to speak).
So it sounds like you have followed the steps for installing SPT using the Automatic Installer, you double-checked that your mods are up-to-date/compatible with the SPT version you are using and removed any problematic mods but are still having the same problem. Are you sure you haven't changed anything in the files? Even for any of the mods you have installed? Sometimes when you adjust things it can cause issues but I'm just asking for clarification.
Please could you upload your logs here in the comments for me and I'll take another look at them.