This is not a Pelles C problem, but it sure presented as one, so I figured I would write it up.
Occasionally when I build a Windows application under Pelles C (running in 32-bit mode on Windows
there would be a looong delay after it displayed "Compacting CodeView information" in the Project tab, and, if I was building and running, an equally looong delay after it displayed "Done." and before the program ran. This was driving me nuts, because Pelles C is usually so responsive, and because small changes to the program source would cause the delays to occur or not occur. A little investigation showed that it is not Pelles C causing the delay, it is the real-time protection service of Windows Defender, which is intercepting the write of the .exe file and doing a ton of computes on it.
The "fix" to this, if you want to continue running Windows Defender, is to exclude the temp directory in which Pelles C builds its executable from Windows Defender scans. This does provide an opening for malware, but a software development system is pretty much indistinguishable from malware anyway. In Windows 8 this directory is
c:\Users\<user name>\Appdata\Local\Temp
(Many applications create app-specific subdirectories in this directory for their temp files,, so should Pelles C)
Richie