When upgrading firmware, I think it's best to use that clean file regardless of whether it came with pirate firmware or not.
The reboot thing has nothing to do with pirate firmware. I'm not sure if it's a hardware or firmware issue.
I've owned 2 Coolsats. My first one came with hacker firmware. I replaced that, and it worked perfectly. No reboots, no issues, other than the original problem with the PVR not working, but that was corrected with firmware updates.
When my first 8100 died in a thunderstorm, my "brand new" replacement 8100 had the rebooting problem right out of the box. Even before I programmed in my first satellite. Ie I FIRST programmed in my OTA channels, and even before I had all of them programmed, it started rebooting. After I had a couple satellites programmed in, I started using it, and the thing would reboot approximately every 30 minutes. I noticed that the unit was hot to the touch, so I assumed that the fan wasn't working, so I installed a computer fan under the unit, blowing up through the holes on the bottom. This cooled it down, a bit, but didn't solve the problem. I later looked through the holes and observed that the fan WAS moving, but I'm guessing that initially it wasn't, and the overheating may have caused some damage.... I'm not sure.
I sent the unit back to the dealer, who sent it to Coolsat, and they sent it back saying that nothing was wrong with it. Tried it out, and it was rebooting every 30 minutes just like before. I put in the most recent (at that time) factory firmware, and it still rebooted every 30 minutes. I then tried a couple versions of pirate firmware.... same thing. Finally, I found a version of pirate firmware, which "seemed" to fix the problem. It stopped rebooting every 30 minutes, but might reboot perhaps once a day or two. Eventually, the new 2025a factory firmware came out, and this performed in a similar way, usually only rebooting about once every day or two....... HOWEVER... this only lasts for a limited time. On using the 8100, it eventually reboots more frequently, and eventually I need to re-flash the firmware. Usually when I re-install the firmware, I get back to the situation where it will only reboot once a day or so (not positive, since I don't watch it 24/7). It almost seems like the more sats I put in it, the quicker it will get back to the situation where it's rebooting every 30 minutes, so I've only been programming it with 2 or 3 satellites that I watch the most, also because I have to program these things in manually, because the channel data recovery thing while better with the new firmware, still doesn't work perfectly.
Anyway, this rebooting thing is so annoying that I've pretty much stopped using the receiver, except when I want to watch something while I'm recording with another receiver. HOWEVER, I WOULD suggest that if you use the CLEAN file, and re-load the firmware, that you might find that it at least temporarily cure the reboot problem. I predict that it will return however.
EDIT: Just wanted to mention that the "rebooting" problem has two manifestations. On MY unit, originally it wasn't a rebooting problem, but instead it first started out as a problem where it would continue to have video, but would lose audio. Then, if I tried with the remote to get the audio back, the first couple of remote keystrokes would work, but after 2 or 3 keystrokes, the receiver would lock up, and I'd have to do the switch off/on thing to reboot it. Eventually, this behavior was replaced by the rebooting problem, but occasionally I'll still see it do the audio thing. It seems like the issue is one where the processor gets confused and can't recover, and either freezes or reboots.