Thanks everyone for your responses. Here's an update based on our visit to the Migration office this past week. Unfortunately the process to fix the problem with our entry/exit records starts with a two-day step. This would have required us to stay overnight in the city just and then come back at 2pm the next day to gather papers and resubmit them with the next set of papers. So we've opted to do that 2nd part next week instead. But we spent the ENTIRE day on this first part.
Ok, so: We've learned that Guatemala does a pretty crappy job of entry/exit record keeping. Separate from the issue that my passport wasn't stamped on the way back into the US is the fact that my last exit last year was also not in their computer system (though my other Guate entries/exits were). Neither was my re-entry this year in April (which I clearly have an entry stamp for in my passport). The problem is far worse for my friend who discovered that there are several entry/exits in the past year+ that while they are in her passport are not in the Guatemala computer system. They appear to make some judgements based on what's in the computer. Clearly the inaccurate/insufficient information is a normal problem since they have a documented process to fix your records in their system. We were only two people of many visiting the office that day that were going through the same laborious process.
I won't go into all details in this post (but can later if helpful to others), but it is a multi step, multi day submission process that takes 30 days for the fix to be applied. They indicated we will get a piece of paper that says the records are being worked on that *they say* will alleviate problems if we try to leave/enter the country during that 30 day window.
I will say a few things about step one in case it's useful for others in the future. Gather all documentation of your entries/exits that you need to prove/fix (though you will probably not know what those are until you go there and get a printout to see what's missing). Clearly if you have saved the exit postage stamp when you fly out of Guatemala, that is great. But I'm not sure how many people save those. I will from now on. In lieu of perfect transport records, you may be able to provide receipts or other documentation proving you were in another country during the window in question. It certainly doesn't hurt to provide more detail if you have it since they are effectively making changes to their official records. We're fixing them all just to be safe since we're already having to go through the process.
We also had to go to an Internet cafe and type a document indicating all this, what specific entries/exits were missing with all the detail (flight info, etc). For me it was only 2. My friend had more since she was in/out frequently last year. This document had to be signed and notarized. We also made copies of all the documentation (flight e-tickets, frequent flyer statements, etc.) and had those notarized (upon advice of a lawyer friend in Guate). We also had to provide a fully copy of every page in our passport and every copied page had to notarized.
The fee for submitting to the process was Q40. There was some confusion from some of the staff on a few things (we made 5 visits to the office that day and wound up talking with every attendant I think). I will say there were pretty friendly and tried to be helpful with us (even though receiving conflicting info at times). I can't remember exactly what got submitted day 1, but I know the bulk of the documentation we wound up only showing to them and then having them tell us we would submit it all next day after we received some other document back from them. This is where we are deferring until next week when we'll return to submit all that documentation together. There is just no way they will let you submit it all the same day.
Like everyone has said, such messes can be avoided if you make sure to get your re-entry stamps to the US when flying (and all other times when available - Guate doesn't exit stamp your passport when flying from everything I've read - just that postage stamp receipt thing which is not part of your passport). I would also say that if you are in question about your records (missing stamps, etc.), I would get a copy of your records from migration so that you can deal with any issues ahead of when you are trying to travel.
As for the document we signed about leaving illegally, etc - they just looked at it and didn't really care about it. Based on the documentation we had with us and they briefly looked at (again, to be officially submitted later), it was clear that it was a records problem.
I will update again after our next visit to Migration to submit round 2 of paperwork to fix our entry/exit records. On the upside, we were at the office on the day they were voting for the "Queen of Migration." Yup

. So there was a pretty positive (almost festive) atmosphere in the building with flyers all over asking workers to vote for various women. And yes, someone was actually crowned queen by then end of the day. We also ate a good amount of gelato available at the mall a few blocks away while waiting.
