Pausing workflow until action complete
Just loaded Hazel v3 on my Snow Leopard (10.6.8) and I noticed that it does a poor job of detecting when a file is busy. 

When I created a file like this...

$ cat &gt; fileXX

In it's log it correctly says that file is busy but then gives up on it and moves it anyway....!?

2014-09-28 22:07:32.735 hazelworker[11272] Processing folder Test
2014-09-28 22:07:34.740 hazelworker[11272] File fileXX is busy. Skipping for now.
2014-09-28 22:07:36.751 hazelworker[11272] File fileXX is busy. Skipping for now.
2014-09-28 22:07:38.756 hazelworker[11272] fileXX: Rule Newly Added Files matched.
2014-09-28 22:07:38.871 hazelworker[11272] [File Event] File moved: fileXX moved from folder Test to folder Test2.


Multiple files are processed as they appear. I even tried adding a delay on the fist file, via applescript, to confuse it but all that did was delay the first file, all other files got processed, one at a time.

On the opposite side, creating a bunch of files in a burst, didn't affect it. Even tried creating and importing into iTunes in a burst - no problems.

So, I'd recommend


Check your Hazel log file for issues. 
Possibly change your rule to process files with Date Added is not in the last x minutes  
Check whether your iTunes is the root cause. First processing may be slow since iTunes takes a while to launch, affecting subsequent files...


If all else fails, try contacting the developer... :(