Above a flag weight score of 500 the increase with each flag accepted as helpful becomes non-linear, with an upper limit of 750.
This effect is unrelated to your reputation score.
The MSO faq page What is flag weight should confirm this, with the original source being here.
However, the flag weight not changing despite your continued flagging is based on what option you're flagging as and your reputation.
As a user with 3000 reputation, when you flag a question to be closed, it will automatically convert it to a vote to close and thus not a flag. This is by design.
You can still flag non-answers, spam and abusive posts as before.
If it's an urgent matter, or requires moderator intervention (such as migration to a site not included in the default options), use the flag other and include a short precis on what the situation is.