When comparing two separate build logs (both being done in its own, different directory), the log line containing protoc shines in the diff:
$ diff -u 7774.log master.log | grep protoc
-/opt/local/bin/protoc --cpp_out=qt --proto_path=/private/tmp/bitcoin-7774/src/qt /private/tmp/bitcoin-7774/src/qt/paymentrequest.proto
+/opt/local/bin/protoc --cpp_out=qt --proto_path=/private/tmp/bitcoin-master/src/qt /private/tmp/bitcoin-master/src/qt/paymentrequest.proto
$
There is no reason to use absolute paths here.
After this change, the protoc command line is always
/opt/local/bin/protoc --cpp_out=qt --proto_path=qt/ qt/paymentrequest.proto
@theuni Please have a look.