Interestingly, make realclean, which one is instructed to use if any issues are encountered in the flash guide, seems to be running into an error as well. make clean doesn't return any obvious error but it remains to be seen if it's actually working as intended.
When probing Makefile.h, located in /groups/dark/tyler/flash/sites/fen.bluegene.bnl.gov/Makefile.h ,  the contents of the file are as follows