This is pure speculation on my part...
I initially had a heck of a time getting it to work with my Dynon EFIS. Turned out the problem was that both the Rx and Tx pins (2 & 3) were connected as I was using standard cabes. The Dynon apparently always puts some data out on its serial port which as soon as the iFly picked it up confused the iFly as to what was connected. I ended up clipping the receive pin off of the USB to serial adapter so that the communication was strictly one way - out from the iFly. Once I did this the iFly correctly assumed the port was purely NMEA out and has been sending happily to my EFIS ever since.
Here's the way old thread on the topic: http://ifly.adventurepilot.com/SUPPOR...
Again, may have nothing to do with your issue, but definately make sure your EFIS isn't outputing anything that the iFly could receieve as soon as it receives something it concludes the port is for something more complex than straight NMEA out.
- Alasdair