For now, try to run BitcoinQt on your own and turn off the 'manage bitcoind' option in settings, see if that fixes it. Also get rid of bitoin.conf in your bitcoin folder if there is one
Further testing proved that transactions weren't showing up until the the first confirmation went through. I did what you suggested goatpig and it did indeed fixed my problem. Thank you.
This works but I'm wondering if Bitcoin-QT is more resource intensive than bitcoind or is the difference negligable?
Edit: LOL I just realized you were probably talking to sdczen rather than me. It fixed my issue just the same though
