As Ulrike Fischer commented, Biber always performs a full compilation run when it is called. Biber does not and can not (currently) detect any changes to do only an "incremental" run or a run only when required (from the .bib and .bcf files).
If Biber is only run when there are changes in to citations or the bibliography, you are already using a script or some other utility that detects these changes and runs Biber automatically.
Chances are that tool is not able to properly pick up the Biber run if Biber's output files are diverted with --output-directory (my guess would be that your tool checks for the presence of a .bbl file, if it can't find one, Biber is rerun, with --output-directory the .bbl is directed into the subdirectory, which is apparently not checked by the script). In particular the fact that you pass the build directory information directly to Biber and pdfLaTeX probably means that your tool/script doesn't even know about the "build directory" and doesn't consider checking there for files. If your tool/script supports "build directories", you probably need to tell it directly.
Don't use build directories: They cause much more trouble than the limited benefits they may have for you.
The problem with "build directories" is that they cause auxiliary files to end up in unexpected places. Stuff simply isn't where everyone expects it to be.
This may not be a big deal when your document only needs to be run with LaTeX, but it can get increasingly frustrating if additional tools like BibTeX/Biber (for the bibliography) or makeindex/makeglossaries (for the index) are involved. Essentially the helper programs assume that the auxiliary files they use to communicate with LaTeX are in the working directory (which should usually be the directory of the main .tex file): They expect to find the auxiliary files written by LaTeX to tell them what to do there and they will write their own auxiliary files that feed certain data back to LaTeX there as well. If you use a "build directory", LaTeX outputs the auxiliary files to the build directory. Now the helper tools won't find those files in the working directory, they need to go to the "build directory" instead. But then the tools need to make sure that they still resolve all other file names (for example of .bib files) relative to the working directory and not the "build directory".
Some tools like Biber have options that help them deal with "build directories" but I wouldn't be too surprised if there were some tools that simply can't handle this discrepancy between working directory and "build directory.
