I am currently working on putting it on our local cluster (again). When fslconf/fsl.sh is sourced FSLMACHTYPE is given a value corresponding to one of these folder. I looked at the difference between linux_64-gcc4.2 and 4.4 and that's not pretty. 4.4 assume a default location for vtk?? which isn't in 4.2. 4.4 set -fopenmp.
I think you should patch fslconf/fsl.sh to return a more generic FSLMACHTYPE that we could control. compiler, flags and so on are defined in there.

Also you are very light on dependencies. fsl will build a number of things by itslef unless you point to a system location. tcl/tk for example. fftw and boost are also asked for. This is all in config/$FSLMACHTYPE/externallibs.mk.