Don't know if this is helpful, but I'm experiencing this isse with a completely new install of KSP, and the only mods I'm using are the latest GPP and pre-requisites (the exact versions listed in installation instructions.
More importantly, I've found a way to avoid the freezing issue (with varying degrees of success) by breaking time warps into shorter sections, so far I've only orbited the two moons in career but the crashes have only ever happened on escape / encounter trajectories, (usually before but sometimes after the transition) never on orbital/suborbital. Once I returned from a mission, I launched another one with the same crew and I haven't had the problem since. I think it may be milestone or milestone-contract related.
A probably unrelated issue: I have only tourists showing up in my astronaut complex and the only recruits that I can hire are the ones for rescue contracts and if I do it they don't actually join (again, no mods other than GPP)