It is hard to help when people don't articulate their problems clearly.
Thank you, I've done that but the situation gets worse! This time I had an Application item on my desktop which I moved to the Applications window - but it never appeared in there and I'd lost it!
Either there is something very wrong with your mac, or you are very clueless about how the mac works - and your last confusing statement seems to suggets the latter:
How can I remedy this for Applications and all the other sidebar items that don't appear where they should? Is this also something to do with Safari Preferences?
It is completely different to drag something to a folder or to the Finder sidebar. You say one thing, then talk about another...
If you don't see "Applications" in your sidebar, you can locate the folder and drag.
But you started saying you dragged an "Application Item" from the desktop... what was it? Where did you drag it to?