First of all, just take a moment to step back and remember: flags are here to inform moderators of what's going on so that we can take special action if necessary. Moderators are for unusual conditions - things that are beyond what regular users can handle on their own. Flag weight is not a big deal. Yours is high enough that one or two invalid flags won't be a problem. Our flag quee is usually pretty short, so your flags will get seen in a timely fashion. Yes, flag validity is arbitrary and subjective. Don't worry about it.
To address these specific flags:
- http://superuser.com/questions/311954/what-enclosure-should-i-get-for-western-digital-caviar-green-3tb-hard-drivehttps://superuser.com/questions/311954/what-enclosure-should-i-get-for-western-digital-caviar-green-3tb-hard-drive
You flagged this with the message "shopping question". Why? You have well over the 3000 rep required to vote to close the question, and it appears that you did not exercise that privilege. Shopping questions are off-topic, so vote to close as off-topic. Unless a question needs to be closed urgently, a flag is really not necessary if the question is merely off topic and you have the ability to vote to close the question. It wastes moderator time when there are flags that should close votes; this is probably why your flag was rejected, even though the question was closed. Yes, the question was off-topic, and your flag was invalid because you should have just voted to close.
"Dual post"... where? In this case, dismissing the flag is a borderline decision. If you had included a link to where the double post was, then it might have been useful, but it was probably rejected for that reason. In this case, the question was closed as off topic, because iPhone questions are not permitted on Super User. You mentioned "probably better on another site", so you must have understood that it's off topic. Once again, you could have just voted to close, instead of flagging.
The line between voting to close and flagging is hardly mysterious. If you think a question should be closed, vote to close it. Only flag a question if it has problems that can't be handled by the standard vote to close system.