Can be a "legitimate" program an APT?

During my researches I found the next file.

 MD5 5e81bd134168d7d8c91b96d88b5e0fd0                                   
SHA1 a632371b2aa54709d4bf6b0f28cb1904cb8864bc                 


The file is the HashCalc application made by SlavaSoft company (or no).

It works as its definition into SlavaSoft homepage:
A fast and easy-to-use calculator that allows to compute message digests, checksums and HMACs for files, as well as for text and hex strings. It offers a choice of 13 of the most popular hash and checksum algorithms for calculations.
And the binary has all features described in its description.


After a static analysis, I did not find anything interesting, just in the ".text" section there is permission to write, but this is typical in some packers.
When I analyzed the binary dynamically, no suspicious behavior was detected, I tried almost all features.
At this point, I was confused, it seems a legitimate binary, if there have not enough time to analyze the file, every people (including me) will say that the binary is goodware.
Before starting to debug the program, I thought to download the file from its homepage and compare it with my binary. But usually when a file is been analyzed we can not get the original file for comparing. In those cases, there are two choices, finish the analysis or to debug the full binary. If the binary is too big, we can spend a very long time to debug it, some times will be almost impossible if we want to have an immediate response(+100MB).
In this case I have the original file but, is there some hidden feature in the program I am analyzing? let's see.
They have the same entry point.

The MD5 value of all sections are equal, except in one case, ".text" section.

Comparing ".text" section we can found the differences between both files at the last bytes of the section.
If we decompile those bytes with hiew, we can read some ASM instrucctions.


I am going to put a breakpoint at the first instruccion, I want to debug that code. Maybe the code is executed or maybe no. Maybe it is not a code.
After put the breakpoint, the application runs well and it does not stop its execution. The images below show me testing some features of the application without stopping its execution.

In the next image, when I try to get the hash signatures from a file, the application stops its execution.

Now we are at the first instruction of the code seen previously. This code tries to decrypt itself. It has an encrypted shellcode

Function for decrypt the shellcode. (It is a simple XOR with 7 value).

Decrypted shellcode.

There are some interesting strings into decrypted shellcode:
- kernel32
- ANNA (Anna Chapman???)
- CreateEventA
- \\.\PhysicalDrive0
- ntdll

The shellcode looks like: