I'm writing a c++ program that takes in input as an exe file, encrypts it (just xoring) and adds the encrypted exe as a resource to another exe (stub).
The stub decrypts the exe and saves it. The problem is that the decrypted exe won't run. The bytes are the same, I can open the decrypted exe in a PE editor, but it just won't run.
Any suggestions?
If the original .EXE and the decrypted .EXE are really the same, and assuming that the decrypted executable is a Windows .EXE file with an .EXE extension (as your referring to .exe and PE format seems to indicate), this might mean you've stumbled into a security feature of some kind.
The behaviour of your program is that of a single-stage malware dropper. It doesn't matter if the decrypted file is not actually malicious: the system cannot know it; it sees an executable that creates another executable and attempts to execute it, and marks it as "do not execute this, ever" (for example via DisallowRun. There are other ways).
It is also possible (and, do not take this wrong, but more likely) that you're actually doing something wrong: the extension is not .EXE, the file is not exactly the same (have you checked the MD5/SHA checksums of the original and decrypted file?), you attempt to run the file while it's still open for writing...
Try looking at the Event Viewer and/or antivirus software log, if any, to see whether this may shed some light. Is this your own development machine, and do you have full Administrator rights to check policies, in case? Also, check and report the error status and/or any error message that you might get from attempting the execution.
