I had the Please Wait... reboot loop issue mentioned by jleavens. I'm writing in the hope that I help somebody out.
I just spent the last two weeks getting familiar with my 5040 innards, rtv_patch, and hard drive upgrades. After much effort and buying a new Maxtor 120GB drive, I believe the answer to my original problem with the 2.5-year-old stock Maxtor 40GB setup was the grounding screws on either the motherboard or power supply.
The original symptom was a show hanging (video freeze with audio in a short loop). After reboot, continued to work normally. One morning after the same issue, unit got into a reboot loop at the Please Wait... screen.
Called ReplayTV folks and they told me for $80 + shipping they would fix it. Ha!
I read up on rtv_patch, ripped the sticker, opened it up and stuck the drive in my computer. With rtv_patch, did a backup, restore and patch to the same drive (lost my shows, but wasn't concerned about it). Put it back in the unit and it booted up and ran fine for a week (good for me, saved $80+) before doing something a little different than before (bad for me, not working again).
This time when it would boot up, it would go from the Please Wait... screen to the Quick Setup screen and then turn off. When I turned it on, it was at the Quick Setup screen prompting me to hit Select to continue. However, the unit would not respond to the remote at all, so I was essentially stuck.
I decided to buy a new drive to see if it was a drive problem. I plugged both the old drive and the new drive into my computer and used rtv_patch to copy the partitions to the new drive. I booted up the new drive and got the same Quick Setup dead end.
I did a restore to the new drive using my backup from 2 weeks prior. Put the unit back together and it booted up! Just for good measure, I did a factory reset and went through the setup flawlessly. Back in business or so I thought.
After checking the Channel Guide to see that things were working, I clicked on System Information in Setup. It hung there for 5 minutes before I manually rebooted. It came back up. 411-Zones indicated that I had September 2003 version. Using 243-Zones, I did a Net Connect. Everything worked fine...it downloaded the new software. When it rebooted however it got stuck in the Please Wait... reboot loop. AAAGH! Back to where I started.
So at that point I had a new hard drive that's essentially been wiped by a factory reset and it still doesn't work. I think it must be the latest software version, since it seemed to work with the 09/03 software. I figure I'm toast.
I start rummaging through this forum this afternoon and come across a thread talking about a grounding problem with the motherboard and power supply due to loose screws. I figure it's worth a shot so I open up the unit one more time and give a little tweak to each one. I plug the unit back in and PRESTO! it comes back to life on the first try. It's been running fine all evening...assuming it continues to work, I end up with 3 times the storage and a great amount of knowledge.