no warning if included header and library dont match

Can you explain your scenario in a little more detail? In C, there is no need for the header and library names to match. The header provide a compiler with interface information regarding the .so file. What warning would you expect a compiler to generically provide, and how?

Matching ABI to header data is exceedingly tricky, to say the least.
http://people.willowgarage.com/straszheim/bydate/110816.abi_compatibility.html

I tried to create a little program with libfann. At compilation time there were no errors, but at runtime it continuously segfaulted. So i created a testcase.
The code of the testcase included "doublefann.h". I tried to compile this testcase with "-lfann", because at that point i was totally unaware of the fact that i had to supply "-ldoublefann". As one could have expected it did not work. "double" is just bigger as float.
As already said i spent two days searching for the answer, until somone pointed it out to me (http://forum.ubuntuusers.de/topic/c-segfault-bei-verwendung-von-libfann/).

All this took place on the same machine, so no differing lib versions:
    Linux hsw-vosteen 2.6.38-13-generic #53-Ubuntu SMP Mon Nov 28 19:33:45 UTC 2011 x86_64 x86_64 x86_64 GNU/Linux

Maybe i am just not skilled enough, but libfann was the obvious choice to link to. But as i was not right, the lib should point it out to me. Somewhere.

If it is not technically possible to inform the user about it at compile/link time, it should be put BOLD into the documentation.

Yes, it is a tricky problem - Personally I would have set it up so that there would be TWO libflann s, which conflict with each other and cannot be installed simultaneously.

However, I would recommend posting a bug, and requesting that a runtime check be made available. It should be possible to create a function that has a signature such as

int getFannPrecision();

which returns "4" and "8", and can be used as a check

if(sizeof(fann_type) != getFannSize)
{
printf("well that isn't right, library and compiled fann size do not agree!")
return someErrorCode;
}

As you have set this as a support request, I would recommend filing a bug with the upstream version of Fann itself, requesting something like the above change, or a more prominent mention in their webpage's documentation.
http://leenissen.dk/fann/forum/viewforum.php?f=2