Unaligned memory access in 2.6.39

Hi guys, This is my first post on KernelNewbies.I have a CGI binary written in c++ which uses some shared objects which use STL. The code is legacy code, so it contains a lot of #pragma packs. I used to run this code on kernel 2.6.33. and I updated the kernel to 2.6.39 and the same CGI binary is giving segafault. (which works on older kernel) But if I remove #pragma packs it works as expected on later kernel too. I am using intel atom processor. Can anyone give me some clue about what can I do ? I know that removing pragmas is obvious solution but its affecting some other code. thanks,Rohit