Thanks to all that have commented. The Linux perl's weren't build with -Duselongdouble and the GCC versions are the same (well, the major points are the same). The same CPU is being used, albeit with the Linux version running under VM. I have tried other machines/OS/GCC versions and I get the same results.

I have started to create smaller test cases. The following is a perl print out from the C structure when run under win32 (regardless of O level) and Linux (-O0) and Linux (regardless of O level) when ran via Valgrind:

170 : -25
171 : 9
172 : -28.0000000000005
173 : 25
174 : -156
175 : 26.0000000000005
176 : -50
177 : 34.0000000000005
178 : 36
179 : -10
180 : 22
181 : -70
[download]

The following is a perl print out from the C structure when ran under Linux when compiled with optimization (1,2 or 3):

170 : -25
171 : 8.99999999999963
172 : -28.0000000000001
173 : 25
174 : -156
175 : 26.0000000000005
176 : -50
177 : 34.0000000000003
178 : 37.0000000000005
179 : -10.0000000000001
180 : 21.9999999999999
181 : -70.0000000000003
[download]

I would expect to see differences of 0000000000003, but if you look at line 178 you'll notice a much larger difference and it's this that is causing the test script to fail. As yet, I dont know what is causing this difference...