Just out of curiosity, did you make sure to choose All Time? Because if not, the default setting when you go to clear is just for like the last hour.
The only significant differences between private window (which is what opens when you do guest window) and normal is that private window opens with all extensions disabled by default and with no cookies. So as you surmised, it should be one of those two issues on your main profile.
Also, when you said you deleted all extensions, did you actually remove them or you just disabled? And do you have any themes you have installed?