Jagex have returned the Perm ban's!

Jagex have never taken away perm bans, they stated that for heavy macroing offenses perm bans are issued and temp bans are issued for lighter macroing offenses. Like you stated you have achieved multiple 99's for botting and were already at 90 hunter, that is a heavy macroing offense and therefore in Jagex's eyes deserved a perm ban.

Also remember that it could take several months after you botted for Jagex to even issue a ban so I think that the ban you were issued was for a previous skill you botted.