OK, seems niggly enough that this is better sorted out in a github issue. Most interesting, I'd think, would be comparing the compile command lines from a

./pants compile ...

- which sounds like it correctly caches, vs a

./pants run ...

. You can get at these by either running with

-ldebug

or 1st running

./pants server

and using the web interface to expand task nodes until you find the zinc ones with gear icons - there will be a command node.