If I remember correctly, when the check engine light is on, it disables the cruise control until the code is cleared.
I have an 05 Sti and I had problems with the cheaper OBDII scanners not reading codes. I found the scanners like the SnapOn and the more comprehensive scanners that provide explanations in their software do a better job of reading the codes.
That was my experience, but I'm a newer Subaru owner after 20 years of owning Honda vehicles.