This is interesting because I have never had any problem buying any of the guns that I have. I was always conditionally approved at the gun show or shop and after the three day waiting period I was always able to pick up my guns.
But my licenese was held up pending verification from the local jurisdiction that an arrest that showed up on my FBI record check was dismissed. So is it safe to say that the check that is done when you purchase a weapon is not as thorough as the check that DOA has done on you for the license?
Both are checks for criminal records but the purchase relies on your name and SSN whereas the CCW process submits your finger prints to the NCIC (FBI criminal records system). Theoretically, in absense of a name or ssn change, they should reveal the same info. The DOA uses prints to verify the applicant IS, IN FACT who he claims to be and not using an alias to hide a criminal record.
The process after the record is retrieved is very different though. The DOA, for license puposes, is mandated to be sure you don't have a disqualifying conviction and the Federally mandated check is required to issue a temp. approval IF they can't verify a conviction, even if one may be still found later. Then they can reverse the approval, issue a denial and turn info over to local LE to have the weapon confiscated and the applicant arrested for providing false info and obtaining a weapon denied to his status.
Since you didn't have a license, the conditional approval was automatic after three days IF no determination was made as to the status of your arrest. It is possible, with a license, you will still be required to wait three days, not as a "cooling off" period but, rather, to satisfy the "default" window FDLE has to either confirm or disprove a conviction.
After the original jurisdiction confirms a non-conviction outcome, a conditional approval becomes an approval or, the reverse, if conviction is found, it becomes a permanant disapproval.
It is very unlikely a licensed carrier will have a conditional approval reversed since DOA already has confirmed a no conviction status BUT the two processes are seperate and kept so in part by privacy laws to protect your status as a permit holder.