The return values from Cwd functions, in your case abs_path, are tainted. Compare:

perl -MScalar::Util=tainted -MCwd=abs_path -T -e '$0 =~ /([\.\/\w]+)/; print "tainted!\n" if tainted($1)'
perl -MScalar::Util=tainted -MCwd=abs_path -T -e '$0 =~ /([\.\/\w]+)/; print "tainted!\n" if tainted(abs_path $1)'

BTW: I find it scary to use taint mode and then allow relative include paths... YMMV.