Slow Startup Issue

Hello to all! I just joined the community and I'm searching for some input with a new Startup issue on my MacMini OSx Lion! Every startup now involves a Grey Screen with the Apple Logo, Spinning Gear and a Progress Bar, delaying the startup to about 3 minutes. Final result is reaching my Desktop and all is well.
It seems that this issue has started after my install of Applejack and running the software to address sudden inability to view any Video on internet. The outcome was successful in addressing the Video problem but I'm wondering if somehow it has now created a New Issue with my Startup being extended/delayed. Any input would be greatly appreciated!

If you're under warranty, take it to Apple.

Otherwise, repair the hard drive using one of the three methods recommended by Apple:
Resolve startup issues and perform disk maintenance with Disk Utility and fsck
(this was a pre-Lion guide - to try Disk Utility, boot from the recovery partition - one way is hold the option key after the gong sound, then choose recovery partition to boot, then find and use Disk Utility to repair the startup Volume.)

If this doesn't work, you'll probably have to reinstall OS X.

Slow Startup

Thank you for the reply and input on addressing this issue. Have you seen this issue before? I ask because, to me, it seems that while startup is successful(although delayed) it appears that with the Progress Bar being visible it is indicating that it is performing some sort of system testing either via an Apple application or a "third party app"? I mean the final result is that it does Boot to the desktop! Again, thanks for your taking the time and sharing your know how!

Try removing Applejack, the instructions were included with the download, and see if there is an improvement. Also checked out Startup items to see if anything is selected which would slow the Mini down?

-- "If this doesn't work, you'll probably have to reinstall OS X."

I followed your suggestions and : Booted from the Recovery Disk and ran the Disk Utility which ran the "Checking File System" which returned "Volume Repaired"! Then ran "Updating Boot Support Partitions" which returned ERROR: Disk Utility can not Repair this Disk! Backup as many files as possible then Reformat your Disk and Restore your Backed-up Files."
So that's where I'm at for now - My most recent System Backup is about 6-7 days old and I plan to use that for my file restore. I can't figure out what caused the damage but hopefully a clean install will solve any and all present issues! Thanks for your input!