Yeah, it's a big problem with this system, so it's not entirely your fault.

I tried to make new stories that really associated a word with a particular context.  Like, rather than thinking of the regular word 'crash', I would make a story about the movie Crash.  Or I would think of a song lyric that used the word, and make my story refer to the song. 

You're failing to distinguish between the two because their meaning is very similar, and that's what your brain is thinking of.  But in something like a song lyric, the actual word that is used is important beyond just the meaning.  In regular conversation you could exchange synonyms, but your brain doesn't do that with song lyrics or titles.

So try to use those kinds of connections

To OP:
some people argue synonymy in the strict sense doesn't exist, so you have to be more visual, and/or use associations. For example:
decline > roman civilization
degenerate > mutant
collapse > dam/building
crash > plane...

But even then, I had problems with some others, and I ended up changing the keyword into something less synonymous.