Drupal 7: Cannot see Module Changes
Unless you are using some sort of opcode cache, the code in your module itself won't be cached. Some hooks will only be run in certain cases and/or have cache. Most likely this is what is giving your problem.

A possible solution would be to uninstall and reinstall it again. (don't just disable the module, but uninstall it). Doing so removes a lot of the information about the module and could fix the problem.

If you gave more detail on the code/hooks you were using, a more detailed answer could be given.

Update

hook_install is run when the module is installed. This is a once per install only, so changing the code after the module is installed won't do anything. A new install is the only way to test the changes, after proper cleanup have been made.