[Yiorgos Moustakis] “What is your experience, is there a difference using an utility like the SD formatter application from the SD Association, than just formatting in camera?”
There is zero difference.
Why would you suspect formatting issues? Formatting issues would have made the footage unobtainable. Let’s take a look at your description of the problem:
[Yiorgos Moustakis] “Everything went fine on the shooting, but upon trying to offload the footage to my computer using my Lexar Professional CF/SD reader I came across the same problem for both cameras”
And then what did you do?
[Yiorgos Moustakis] “The way that I found around that, was to put the SD into the camera that was shot with and make the transfer from the camera’s usb.”
You were having problems reading files from the card in your Lexar reader, and then you put your card into a different card reader (i.e. your camera) and then it worked fine. Doesn’t sound like formatting issues to me.