Let me clarify. First of all, the GPLv3 notice in 
autorevision.cpp as well as the "part of Code::Blocks" sentence is technically wrong (it's "GPLv2 or later", and it is not part of Code::Blocks). However, I don't really mind what license it is, so let's just leave that as it is.
The file 
autorevision.h has no license at all, and it shouldn't have one. While 
autorevision was programmed with Code::Blocks in mind (and has seen some modifications due to specific needs), it wasn't made especially and exclusively for just this one project. It was written as a (micro-)tool to get a revision number hardcoded into a program automatically. That was at a time when no such thing existed otherwise (in the mean time, there are a few tools that do the same, and better).
Someone who uses 
autorevision in a different project (which might not be GPL compatible at all) may not want to have his files automatically tagged with a GPL license.
Also, 
autorevision.h does not contain any original work, it is merely a file that is generated from a project's revision number, so it is really not justifiable to attach a license to it. If that was the case, one could argue that every project managed with Subversion falls under the Subversion license, too.
I don't know exactly what 
autorevision.h.in does (since I'm no autotools user). In fact, I didn't even know it was there 

Apparently, it is meant to mimic/provide an 
autorevision.h file for tarballs  (I faintly remember someone did something for that some time in the past).
To address your problem, one solution would be to move the comment to the end of the 
.in file or remove it alltogether, both of which will make the file compliant. The other (probably better) solution would be to 
either use the 
.in file 
or run 
autorevision, but not both.