checkinstall just runs make and make install and automake system uses different object-location, so building inside C::B does not make any difference.
I have build C::B 7126 some days ago on my server and all went fine.
It's always a build in a clean environment, so there can be no substantial problems.
We had changes in scintilla, so oBFusCATed's hint is most likely correct. If files have been added (or removed) ./bootstrap is required to rebuild the Makefile.in's from Makefile.am and the configure-script from configure.in and others.
Running ./configure creates the needed Makefile's from the Makefile.in's.
I always run ./bootstrap to be sure everything is uptodate.