Human language is almost never as precise as we would perhaps prefer. A precise analysis of the two sentence yields, as you point out, two possible distinctive meanings. But I cannot imagine anyone actually making the distinction -- they are for all intents and purposes the same sentence.
As to why this might be so, I cannot answer. But as a 61-year constant user of English I can certify I and virtually everyone else would not find these two sentences to mean two very different things.
Consider the alternatives: “I thought I'd never see you again” vs. “I never thought I'd see you again”.
The former suggests that an active thought existed about never seeing the person again, the latter suggests no thought about the subject of seeing the person again even occurred. The problem is related to not thinking about red elephants. Can it truly never have crossed your mind that you wouldn't see the person again? It implies an absence of thought that probably cannot exist.
I am a computer programmer, so I know I can write code that is that is that exclusive, e.g. the computer will never consider that A == B if I don't write it. Human beings are not programmable. If you apparently blew yourself up in my presence, I cannot avoid an active thought relating to not seeing you again. If I merely hear that you blew yourself up, the same. The only case in which I am not going have such an active thought is if I don't hear anything about your fate. It's a null program in that case, and I am also not going to think the first thought either.
Off-topic: does your code really suck? If so, why?