When I checked it just now it had been sitting for about 5hrs. When I checked it the first two times after I did the flush, it had been sitting over night.

If coolant level changes from one time to the next and the motor is cold each time the level is checked (overnight), then there may be issues. Start with a new brand name rad cap. Again, the rad cap is a critical part in the coolant recovery system.

I'm wondering if the funky 'safety release' cap I have on there is making it act funny. I grabbed a regular one from Autozone on my lunch break. Once it cools down I'll throw that on there and watch the levels for a couple days.

If there are no leaks, any idea where to coolant went?

Very possible. Like I said they are garbage and don't work most of the time. Put the new one when it cools and keep an eye on the level.

There may have been some air trapped in the system after the fill. Open systems will self burp so you don't have to do anything but watch level for the first several heat/cool cycles.

Make sure radiator is full, put your new name brand 16# cap on and fill reservoir to line.

Check the radiator, not just the reservoir, when cool after the next couple of cycles. If radiator is full and bottle is down, fill bottle to line. If coolant continues to disappear after a couple of cycles, you may have a problem. Let us know.

I will add FWIW, I don't what other years and systems do, but my '93 normally puts very little coolant into the bottle after a hot shutdown. I just mention this, partly out of curiosity. I know that various temps involved can affect this along with cap efficiency.

Thanks. I'll keep an eye on it and let you know in a couple days.

So after a few days, I haven't noticed a big loss in coolant, but I have noticed a little. It was up to the 'full' line, and now it is just a tad below. Not sure if this is enough to worry about or not.

However, I do have a new development, and I am not sure if it ties into this or not, but it is troublesome. Lately it has been starting rough and idling low. When I say rough, I mean I turn it over and it putters and struggles to get the RPM up. I has been doing this for a couple weeks, but lately it has gotten worse. Then on take off, it hesitates a bit before it goes. Then until it is warm, it idles at what I would guess to be around 500RPM. For the most part, it only does this on the first start/drive of the day, after it has sat over night. It also does it sometimes if I start it shortly after the engine was turned off hot. For example, today on my lunch break, I drove around for a while running errands, and then stopped to grab food. When I shut the engine off it was at 210. When it is warm like that and I shut the engine off, it gets hotter before it gets cool because the e-fan is not on. So if I start it again shortly after I shut it off warm, the temp gauge shows it at 220ish and the e-fan immediately kicks on and cools it down, but the engine studders quite a bit and struggles to get going.

Any thoughts? I have recently cleaned both the TB and the IAC, so I don't think it's that. I have also recently replaced the TPS.

1. Replace radiator cap with dealer, 16 psi

2. To determine if there is daily coolant loss, check cold after it has sat overnight. The coolant level will rise and fall as you drive it. Heat causes pressure in the system that will cause some coolant to end up in the overflow jug and as the engine coolants, vacuum will draw it back into the radiator/engine. There can be vacuum present for many hours so its best to check in the morning after its been parked overnight.

3. Compression test to see if your rough starting is mechanical or electronic

4. Look under the oil filter cap and look for any cracks, tan lines, or discoloration. The place these 0331 heads crack all the time is right there under the filler cap. You may not get milky build up or chocolate milk shake oil if the head only has a small crack.

5. Check radiator and condenser for air blockages (bugs, stones, sand, dirt). A radiator can either be clogged internally or externally. If it is the original radiator, there is a reasonable chance a replacement will give better cooling system performance. Hard to go wrong with the Auto Zone radiators for $110 with lifetime warranty.

Well, I dropped the Jeep off at the garage last night. Today they ran a compression test on the head. Here is what came back:

1: 150
2: 140
3: 140
4: 150
5: 150
6: 150

They are going to run another compression test while the engine is hot, to see if those numbers change. I'll post those as soon as I find out.

Any thoughts?

I received the second pressure test reading, with the engine hot, and he got the same numbers. We are both sort of baffled as to where the coolant is going. With those numbers, is it possible that there is a very small crack? Any ideas?

Those numbers are fine. Until you do some of the other things suggested there is not much else to offer. The lunch time runs aren't conclusive.