When it comes to flags, it is not a simple count threshold, instead, it's a matter of the quality of your flagging. If you flag in an abusive manner, the automation removes your ability to flag. If you flag in a beneficial manner, the automation also notices your attempt to help control spam and abuse. Since the goal of the automation is to prevent abuse, I won't go into any more details. A few vague details were mentioned publicly a few years ago, but the system is constantly evolving, so things have undoubtedly changed.
I do a significant amount of flagging of spam/bad submissions on the 'new' page, and occasionally, I'll flag comments. I'm certainly not perfect, and occasionally, I get it wrong, but I just do my best. Since I've done this for a long time and have a history of flagging appropriately, the automation has never removed my ability to flag, The same is true for the humans involved; none of the mods or pg himself have asked me to stop, or removed my ability to flag.
If you made some bad flags and the automation kicked in to prevent abuse by removing your ability to flag, then don't take it personally. Also, pg has an interesting habit of leveraging time in interesting ways. The only publicly known examples are in the news.arc source and in the Guidelines/FAQ (at the bottom of the page) regarding how rank is calculated. This hints at possible good news; the removal of your ability to flag might be temporary. If it doesn't show up again after six months of "good behavior" then you're probably stuffed or you've hit a glitch.