Recording Drops readings for 5 seconds at a time

[FUBARSS]

When i am recording data logs the software seems to lock up for about 5 or so seconds every couple of seconds. I can't seem to figure out why. I have other data logging software on the computer that doesn't do this, so i'm pretty sure that the computer is not the problem. Is there a possibility that the ECM is not putting out a consistent reading for the log? I've attached a log so you can see what i mean.
shaggy intermittent connectivity.hpl
Also, when i try and manually control parameters in the manual control section nothing happens.

I have also re-flashed the computer to see if maybe it was a bad flash on the tune.

I'm trying to determine whether the ecm is bad, or if it's a wiring issue. i got a p0606 and p0607 before, but i cleared them and they haven't come back, so i'm not sure.

[Ford46Modular]

Did you figure anything out? Mine will scan for maybe 2 minutes and drop out completely. I'm using USB. I've used ELM327 flawlessly for the past year over bluetooth, so I don't think anything is wrong with the car's wiring.

Edit... I just used the MPVI2 on my Buick. It worked perfect. I must have a wiring or ECM problem with the Mustang.