Stale Assemblies and Runtime

I noticed a strange thing when I was working on my project:

Sometimes my code would run exceptionally slow with no rhyme or reason. I suspect this is due to the fact that the "compiled" code was out of sync with the source (I was jumping between GIT branches and hosed some things up is what I figure) as when I would make some changes while monitoring the Editor log file, it wasn't recompile some things. Once I forced a recompile by reimporting the source, the speed picked up drastically back to what I would expect. Without the reimport though it looked like Unity thought the assembly was up to date.

Now, the source code itself wasn't changing (outside of random whitespace/junk changes to attempt to force a recompile) so it wasn't related to that.

Does anyone have an explanation for this or suggestions as to why this would happen? Again, the compiled code would run just as normal but slowly is all. Very strange.