Computer questions

[5speedcobra]

I recently got a whole bunch of spare parts for 98 XJ, including a spare computer. 
So, I wanted to plug it in and see if it works. The jeep fired right up, runs fine, BUT the check engine light was on.
So, I plugged in my scanner... unlike when I erased a code on my original computer; now the scanner was asking what kind of car its plugged into, and then said no codes found...yet my check engine lights still on...
Put the original computer back in, jeep runs just fine, and check engine lights off.  Mine's a 5 speed, and I don't know if the computer is from an auto or 5 speed.

Anyone had that happen to them before? OR any ideas what might be causing it?

Thanks

[apeman]

It'd most likely br an auto ecm
 I put a 5speed ecm in mine and while it ran fine,it kept telling me to shift. Until it finally just held a c.e.l.

[apeman]

I have a spare 5 speed ecm if you ever want to trade for your auto ecm. Lol