I am not an attorney, but I can read English, and below is my interpretation of the law.
First the relevant statute, 790.06(6)(c):
(c) The Department of Agriculture and Consumer Services shall, within 90 days after the date of receipt of the items listed in subsection (5):
1. Issue the license; or
2. Deny the application based solely on the ground that the applicant fails to qualify under the criteria listed in subsection (2) or subsection (3). If the Department of Agriculture and Consumer Services denies the application, it shall notify the applicant in writing, stating the ground for denial and informing the applicant of any right to a hearing pursuant to chapter 120.
3. In the event the department receives criminal history information with no final disposition on a crime which may disqualify the applicant, the time limitation prescribed by this paragraph may be suspended until receipt of the final disposition or proof of restoration of civil and firearm rights.
So, according to 790.06(6)(c) DACS has 3 options total when processing an application:
1 - issue the license within 90 days
2 - deny the application within 90 days solely if the applicant is not qualified
3 - the 90 day time limitation may be
suspended until receipt of final disposition or proof that any initial adverse information that appeared to be disqualifying is in fact not disqualifying
The law does not say that if there is a suspension of processing that the 90 day time limit is out the window and they have unlimited time. It says the 90 day time limit is
suspended until "receipt of the final disposition or proof". If they are in receipt of such final disposition or proof, and if they have by their own admission lifted the suspension, then the clock is running again.
And it doesn't start over from zero either because that's not what "suspend" means. "Suspend" means if at day 42 they discover an apparent disqualifier the clock stops at 42 days
until the issue is researched and a disposition is reached. A that point, assuming the outcome is in your favor, the application is no longer suspended and the clock starts counting again, starting at 42, which leaves them with 48 days left to do #1 or #2 (issue the license or deny the license for cause). If they find another issue they can suspend again while it is researched, but otherwise they only have 90 days total, plus the actual duration while the application is suspended.
If they do anything other than that then in my opinion they have violated the law and can be compelled in court to issue your damn permit. If they have a formal policy to the contrary then I would argue that they have a policy that violates F.S.
790.33(3) and the person or persons who made or enforced such regulation are financially liable and subject to removal from office by the governor.
Of course by the time you did any or all of that they may have simply issued the permit, but this is garbage and should not be tolerated. I'd sue them over it on the principle of the matter.