make sure that the same compiler flags are used too

Good point - I now recall being tripped up by different optimization levels in the past.
However, I think the OP has probably already followed that advice by having built the executable with:

gcc -s -O2 -DWIN32 -fwrapv -fno-strict-aliasing -mms-bitfields -o fite
+st.exe fitest.c -lfreeimage
[download]

Maybe there's some other pertinent option that has been omitted. We can't tell unless we see the output of perl -V:ccflags

There must be a Makefile somewhere created by Inline::C

Also a good point - it's usually under the ./_Inline/build directory, but you'll need to configure the Inline::C script with CLEAN_AFTER_BUILD => 0 to prevent the Makefile being automatically deleted when the compilation successfully completes.

Cheers,
Rob