This has happened before but I really noticed it now. Updted to build from 03-Apr. All files in all directories. (I carried over my CSS and noted the couple of changes to images.php in the new files). However, when I go to my site/zp-core, I am not being prompted to update the files (databases?). It is still saying build 1382 which trac says is from 01-Apr, my last update.

Cleared cookies & cache before I go back to my site.

Well, that means that somehow you did not get everything uploaded from the build. (That is likely to cause problems.) The only suggestion I can make is that you make a copy of your zp-config.php file somewhere outside of the installation. Then delete the folders zp-core and theme. Then upload the new release. Then at least, if a file does not get uploaded it will be missing rather than the wrong version.

When you have updated to a new nightly build you should ALWAYS be taken to the setup.php program. If that does not happen, then something went wrong with the upload.