Custom.css is independent file and any changes applied there should take place imminently. If they don't it means that there could be Joomla! caching enabled... also in some browsers e.g FireFox css files are cached by browser. Then you need to clear browser cache after you change something in css CTRL+F5.
I use custom.css all the time and we suggest other user to do it too. You're first user that reports that issue.
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I think it may have something to do with T3's caching system. On the older Joomla 2.5 there was a button to flush T3's cache. There's nothing like that on this version of T3.
I also use a CSS development tool for Apple Safari called Quick Style.
I can't thank you enough for helping me flesh this out. I have dumped the cache in Joomla... I do an Option Refresh with Safari on the mac.