CFLAGS and CXXFLAGS should be specializations of CPPFLAGS, not the over way around.
diff --git a/templates/Makefile.template b/templates/Makefile.template
index bf36476..5493447 100644
--- a/templates/Makefile.template
+++ b/templates/Makefile.template
@@ -348,20 +348,20 @@
   OPENSSL_LIBS = ssl crypto
   endif
 
-  OPENSSL_ALPN_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/openssl-alpn.c $(addprefix -l, $(OPENSSL_LIBS)) $(LDFLAGS)
-  OPENSSL_NPN_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/openssl-npn.c $(addprefix -l, $(OPENSSL_LIBS)) $(LDFLAGS)
-  ZLIB_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/zlib.c -lz $(LDFLAGS)
-  PROTOBUF_CHECK_CMD = $(CXX) $(CXXFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/protobuf.cc -lprotobuf $(LDFLAGS)
+  OPENSSL_ALPN_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/openssl-alpn.c $(addprefix -l, $(OPENSSL_LIBS)) $(LDFLAGS)
+  OPENSSL_NPN_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/openssl-npn.c $(addprefix -l, $(OPENSSL_LIBS)) $(LDFLAGS)
+  ZLIB_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/zlib.c -lz $(LDFLAGS)
+  PROTOBUF_CHECK_CMD = $(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $(TMPOUT) test/build/protobuf.cc -lprotobuf $(LDFLAGS)
 
   endif # HAS_PKG_CONFIG
 
-  PERFTOOLS_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/perftools.c -lprofiler $(LDFLAGS)
+  PERFTOOLS_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/perftools.c -lprofiler $(LDFLAGS)
 
   PROTOC_CHECK_CMD = which protoc > /dev/null
   PROTOC_CHECK_VERSION_CMD = protoc --version | grep -q libprotoc.3
   DTRACE_CHECK_CMD = which dtrace > /dev/null
-  SYSTEMTAP_HEADERS_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/systemtap.c $(LDFLAGS)
-  ZOOKEEPER_CHECK_CMD = $(CC) $(CFLAGS) $(CPPFLAGS) -o $(TMPOUT) test/build/zookeeper.c $(LDFLAGS) -lzookeeper_mt
+  SYSTEMTAP_HEADERS_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/systemtap.c $(LDFLAGS)
+  ZOOKEEPER_CHECK_CMD = $(CC) $(CPPFLAGS) $(CFLAGS) -o $(TMPOUT) test/build/zookeeper.c $(LDFLAGS) -lzookeeper_mt
 
   ifndef REQUIRE_CUSTOM_LIBRARIES_$(CONFIG)
   HAS_SYSTEM_PERFTOOLS ?= $(shell $(PERFTOOLS_CHECK_CMD) 2> /dev/null && echo true || echo false)
@@ -1194,12 +1194,12 @@
   $(OBJDIR)/$(CONFIG)/%.o : %.c
   	$(E) "[C]       Compiling $<"
   	$(Q) mkdir -p `dirname $@`
-  	$(Q) $(CC) $(CFLAGS) $(CPPFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
+  	$(Q) $(CC) $(CPPFLAGS) $(CFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
 
   $(OBJDIR)/$(CONFIG)/%.o : $(GENDIR)/%.pb.cc
   	$(E) "[CXX]     Compiling $<"
   	$(Q) mkdir -p `dirname $@`
-  	$(Q) $(CXX) $(CXXFLAGS) $(CPPFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
+  	$(Q) $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
 
   $(OBJDIR)/$(CONFIG)/src/compiler/%.o : src/compiler/%.cc
   	$(E) "[HOSTCXX] Compiling $<"
@@ -1209,7 +1209,7 @@
   $(OBJDIR)/$(CONFIG)/%.o : %.cc
   	$(E) "[CXX]     Compiling $<"
   	$(Q) mkdir -p `dirname $@`
-  	$(Q) $(CXX) $(CXXFLAGS) $(CPPFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
+  	$(Q) $(CXX) $(CPPFLAGS) $(CXXFLAGS) -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
 
   install: install_c install_cxx install-plugins install-certs verify-install
 
@@ -1782,7 +1782,7 @@
   $(OBJDIR)/$(CONFIG)/${os.path.splitext(src)[0]}.o : ${src}
   	$(E) "[C]       Compiling $<"
   	$(Q) mkdir -p `dirname $@`
-  	$(Q) $(CC) $(CFLAGS) $(CPPFLAGS) -std=c89 -pedantic -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
+  	$(Q) $(CC) $(CPPFLAGS) $(CFLAGS) -std=c89 -pedantic -MMD -MF $(addsuffix .dep, $(basename $@)) -c -o $@ $<
   % endfor
   % endif