pulling in a snippet of HTML code stored in an external file that contains some javascript (mainly form validation).
Avoid doing this. Writing <script> to innerHTML doesn't cause the script to get executed... though moving the element afterwards can cause it to get executed, at different times in different browsers.
So it's inconsistent in practice, and it doesn't really make any sense to include script anyway:
when you load the same snippet twice, you'd be running the same script twice, which might redefine some of the functions or variables bound to the page, which can leave you in extremely strange and hard-to-debug situations
non-async/defer scripts are expecting to run at parse time, and may include techniques which can't work when inserted into an existing document (in the case of document.write this typically destroys the whole page, a common symptom when trying to load third-party ad/tracking scripts).
Yes, jQuery tries to make some of this more consistent between browsers by extracting script elements and executing them. But no, it doesn't manage to fix all cases (and in principle can't). So don't ask it to. Keep your scripts static, and run any binding script code that needs to happen in the load callback.