Are Drupal .php files associated with a module cached?
To answer it literally - probably, yes, on many levels:


Filesystem cache
Opcode cache
Possible other caches, depends on your configuration


Above caches should not create the effect you are seeing, but outout of the whole page is also cached, in your browser. Inspect headers to make sure it was not the case, and if so, clear caches and try again. If you have any proxy or reverse proxy, make sure they are not interfering, too.

If you are sure pages are not cached at output, and you didn't make Drupal to cache your variable, it shouldn't be cached. So there are two options:


Problems with include path:


  Files are included based on the file path given or, if none is given, the include_path specified. If the file isn't found in the include_path, include will finally check in the calling script's own directory and the current working directory before failing. 


Maybe there is another instance of this file somewhere, one that gets higher priority in including? That's one of the reasons to use module_load_include instead.
Problems with uploading. You know what you sent to your server. But have you inspected (from console, for example) what really is there? Maybe you are looking for something that isn't even there.