I've used Kaspersky for years and never seen a trojan alert for files built in Code::Blocks, although Kaspersky is very much capable of not only making compile times 200% slower (even when disabled), but also of making the entire computer unusable. Kaspersky is worse than any malware you might have, in my opinion.
At one point, Kaspersky insisted that every single file on my computer was possibly infected (including text files...). That was the day I switched to Avast.
To give a figure of the impact, compiling with Kaspersky installed and all build tools and the devel folder whitelisted adds 2 1/2 minutes to building Code::Blocks on this machine (as compared to the same machine with no AV software). Compiling with Kaspersky installed and live scanning disabled adds 2 1/2 minutes likewise. Compiling with Kaspersky installed and globally turned off is miraculously faster, but still adds 2 minutes.
Roughly 60-65% processor use using 5 parallel jobs.
Compiling with Avast! having build tools and the devel folder whitelisted adds 4-6 seconds to the build time. Roughly 95% processor use using 5 parallel jobs.
Adding a folder to the exclusion list in Kaspersky will make alerts go away, but will not address the performance issues. These come from the apparent fact that Kaspersky hooks somewhere in the IO layer and pipes all input/output through a single sequential pipe, optionally scanning it (everything serial, and single-threaded).
