I have had Malone's tunes on my '03 built Jetta ALH, both of my 335D's (2.9), and my ML350 Bluetec (OM642) and have never had any issues with them. No communication errors, no flashzilla (v2 and v3) errors, no tuning issues, etc. I'm very happy with them and I just bought a '14 Golf and I just loaded a 0.5 tune to it and will do the stage 2 when my downpipe comes in. Malone all the way for me.
InfoSec, this is for a stage 4. I've never had any complaints with Malone Tuning tunes on the 0-2 stage tunes. Well, my stage 2 flashzilla was acting up, but not the tune. Its a load tune to car and forget. So, any problems with the flashzilla will be noticed only when you need to remove or install a tune.
My stage 4 was completed over a year ago and I'm quite happy with the results. I no longer contact Malone Tuning, but only because the tune is loaded, and I have had 0 issues. It is very reliable and mileage has been jaw dropping. Last month, on a cross country trip, I averaged 57.1 mpg. Tire pressure at all 4 corners was 41 psi. I'm running Rotella T-6 5w-40 with 0 issues. The stage 4 added to the vw jetta completely transforms the car. If you decide to go this route, be patient with Malone Tuning, and try to find an installer that has installed at least one of these stage 4 kits on your car. You'll be glad you did. This thread can be closed, I've vented my frustrations, and Malone Tuning has made good on their promises. I am happy, and encourage others to become part of the limited individuals that have gone this route.