So I've had this issue since I got the car a few years ago...
Basically I have a check engine light but I get no faults when I plug in a reader, and when I clear the light it will come back after about 3 restarts of the car.
I'm pretty sure it's something to do with the Readiness Monitor, and that it can't complete the EGR test at start up for some reason.

But everything works fine on the car, emissions are fine, plenty of power, and I replaced the EGR valve last year but it made no difference.
I did check the wires going to the EGR and if I remember correctly I had 5V, ground, and 2 signal wires that seemed to "do stuff" when I revved the car, so it seems the EGR is working fine. And if it wasn't I'd probably get a fault.

Since everything is working perfectly fine, it's pretty hard to diagnose it.

Anybody experience anything like this, or have any ideas on how to proceed?

This is a video of my new EGR when I was installing it, with the wires connected, and it seems to be working fine:

 

gijoe, I would say you need to get a more advance code reader. Most "cheapo" (ie, under $100) code readers only read P-Codes. Some may do some random other codes. But, you have the potential to have B, U, P and C codes. So, getting an error code like say C1155 (front wheel speed sensor) would trigger the check engine light (as this would be affecting the speedo and ABS systems), but if your reader can only do P-codes, it will see it as nothing happening. This is where the higher end readers will read all 4 types of codes and give you a truely complete list of errors. If you have the SDD software, that will give you all 4 types of codes too.

 

The reader I usually use is the iCarsoft reader.
But I also had the SSD software (until my laptop died last month) and that was the same when I ran scans last year, no other codes, except the P1000 (see screenshot below). Unless I was reading it wrong or something..
But I did run the EGR test too, where you have to let the car warm up and then keep the revs at a particular level for a few minutes, and I think that also said there was a problem too, but it never told me what the problem was. I think it, like, failed the 4th test of 6 or something like that, I can't remember exactly.

 

gijoe, if your SDD is not picking up anything, then I would give the car a good bill of health. In my mind that really only leaves one other problem, you have a bad instrument cluster and that it is somehow failed to trigger the CEL every once in awhile, driving you bonkers. That is the only othe answer I can tell you.