Just some things to consider:
Whether or not the FlashPaq is traceable (and it most likely is, most newer PCMs keep a record of every time they are updated), it's a flash program, which overwrites and stores the factory tune. You can only do this so many times before your PCM cannot retain ANY information. If you had an original Playstation and had a memory card crap out on you, it's the same issue. If the PCM has been found to have been tampered with, kiss your power train warranty goodbye.
If you should happen to take your Jeep in for service and they have software updates for your vehicle, they will apply them and overwrite your FlashPaq tune. So basically, you want to put the stock tune back on your Jeep EVERY TIME you take it in for ANY service, or you're left with a $300 paperweight that you can't re-sell.
These tuners only work on one vehicle at a time, so if you're thinking you can buy it, use it and flip it, you can't unless you put your vehicle's stock tune back in.
No matter what people tell you about how much faster their car FEELS, tuners can legally only alter parameters at full throttle. Things like throttle response can be changed, which is most likely the faster "feeling" people get, but air/fuel and timing can only be changed for WOT operation. These tables are typically pretty optimized for a stock vehicle, so altering them is only going to get you a few horses at best. You would notice more of a difference with a tuner after doing headers, exhaust, CAI, stuff like that. But then, you'd be better off with a custom tune from a reputable shop for your exact setup. Ask yourself, are you really that concerned about WOT operation in a Jeep?
I used a FlashPaq on my old Magnum R/T and was pretty underwhelmed by what it did for me. It felt a tiny bit quicker at WOT and I gained maybe 1mpg tops, but it also made the car "buggy" at certain rpms and made the idle rough sometimes. They're just not worth it IMHO.