Bare-bones ATMega328P-PU Bootloaded w/ Arduino and desired fuse-settings w/ "ArduinoISP" example in IDE. (more detailed info on that process in this post) Using this programming shield: Yet Another Programming Shield
Testing has shown this much to be working just great. (I'm able to bootload w/ desired fuse settings no problemo)
If I upload my Arduino sketch via "upload using programmer" (aka: If I upload my sketch using the shield I am using for programming) there is an anomaly from when I upload my arduino sketch via ISP (aka: if I remove the freshly bootloaded chip, and upload a sketch via ISP with the FTDI Basic from Sparkfun)
The Lock Byte and Clock Calibration Byte differ.
The reason I found this anomaly:
If I uploaded my Arduino sketch w/ either approach (programmer vs ISP) it works. The sketch runs. Everyone's happy.
BUT... If I upload the sketch with one approach, I cant upload any sketches on that same microController via the other approach.
I recon this problem stems from the anomaly I pointed out.
(I'm using Nick Gammon's Fuse Checker by the way... as seen in the screenshot)