No. This is jumping to conclusions similar to:
Clock Attack (swdate not correct on original and clone) - #4 by Patrick
KVM installations instructions are lengthy and complicated. I’d say these are for advanced users only. There could be localized software configuration issues or even hardware specific issues. If KVM works for you, great. If it doesn’t, feel free to post here but as you can see there’s very limited deep troubleshooting and user support available here if you run into a complex issue.
It would probably require several weeks or months of self-education to acquire the technical skills to understand and fix this. If you like to dig deep into this, consider joining a (local or remote) Linux user group to learn more about Linux. If/when you’re able to create your own Whonix from scratch, chances are great you’d be able to analyze and fix this specific issue too.
Not sure how realistic that is but better than keep you hanging and wondering if you’re being specifically targeted by powerful adversaries. Could be the case in theory but as said, I don’t see evidence for that. Just complex software and usability issues.
Might be useful too to learn how malware actually works. There are videos on youtube etc. showing demonstration of trojan horses. Computer compromise by malware doesn’t work in ways that users can witness. Not by looking at some logs or by having weird issues. It’s completely invisible to the user sitting in front of it. Meanwhile, if infected by a trojan horse, the attack can upload/download any file.